# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0634 numbered 1 through 140 Created new target T0634 from T0634.a2m # command:CPU_time= 5.894 sec, elapsed time= 6.202 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lufA/T0634-3lufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lufA expands to /projects/compbio/data/pdb/3luf.pdb.gz 3lufA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 152, because occupancy 0.3 <= existing 0.700 in 3lufA Skipped atom 154, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 156, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 158, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 160, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 162, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 164, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 166, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 168, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 188, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 190, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 192, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 194, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 196, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 198, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 200, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 202, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 204, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 508, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 510, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 512, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 514, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 516, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 518, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 520, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 522, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 524, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 602, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 604, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 606, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 608, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 610, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 612, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 614, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 616, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 651, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 653, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 655, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 657, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 659, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 661, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 663, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 665, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 667, because occupancy 0.300 <= existing 0.700 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 793, because occupancy 0.300 <= existing 0.700 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 795, because occupancy 0.300 <= existing 0.700 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 797, because occupancy 0.300 <= existing 0.700 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 799, because occupancy 0.300 <= existing 0.700 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 801, because occupancy 0.300 <= existing 0.700 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 803, because occupancy 0.300 <= existing 0.700 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 805, because occupancy 0.300 <= existing 0.700 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 807, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1073, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1075, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1077, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1087, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1089, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1091, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1093, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1095, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1097, because occupancy 0.300 <= existing 0.700 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1151, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1153, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1155, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1157, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1159, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1161, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1163, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1165, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1167, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1222, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1224, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1226, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1228, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1230, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1232, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1234, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1236, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1238, because occupancy 0.300 <= existing 0.700 in 3lufA Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1279, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1281, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1285, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1287, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1289, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1555, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1557, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1559, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1561, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1563, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1565, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1567, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1569, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1571, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1573, because occupancy 0.500 <= existing 0.500 in 3lufA Skipped atom 1575, because occupancy 0.500 <= existing 0.500 in 3lufA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1642, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1644, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1646, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1648, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1650, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1652, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1654, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1656, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1658, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1719, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1721, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1723, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1725, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1727, because occupancy 0.400 <= existing 0.600 in 3lufA Skipped atom 1729, because occupancy 0.400 <= existing 0.600 in 3lufA # T0634 read from 3lufA/T0634-3lufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lufA read from 3lufA/T0634-3lufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lufA to template set # found chain 3lufA in template set Warning: unaligning (T0634)Y125 because last residue in template chain is (3lufA)Q246 T0634 3 :LKKILIIDQQDFSRIELKNFLD 3lufA 122 :QIEVLVVDDSRTSRHRTMAQLR # choosing archetypes in rotamer library T0634 25 :SEYLVIESKNEKEALEQIDHHH 3lufA 145 :QLLQVHEASHAREALATLEQHP T0634 47 :PDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 3lufA 168 :IRLVLVDYYMPEIDGISLVRMLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHNLEALE Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lufA/T0634-3lufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3lufA/T0634-3lufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lufA read from 3lufA/T0634-3lufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lufA in template set Warning: unaligning (T0634)Y125 because last residue in template chain is (3lufA)Q246 T0634 4 :KKILIIDQQD 3lufA 123 :IEVLVVDDSR T0634 14 :FSRI 3lufA 134 :SRHR T0634 19 :LKNFLDSE 3lufA 138 :TMAQLRKQ T0634 27 :YLVIESKNEKEALEQIDHHH 3lufA 147 :LQVHEASHAREALATLEQHP T0634 47 :PDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3lufA 168 :IRLVLVDYYMPEIDGISLVRMLRERYSKQQLAIIGI T0634 84 :SSEHKEA 3lufA 204 :SVSDKRG T0634 93 :NGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 3lufA 214 :RYLKQGANDFLNQPFEPEELQCRVSHNLEALE Number of specific fragments extracted= 7 number of extra gaps= 0 total=10 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lufA/T0634-3lufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3lufA/T0634-3lufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lufA read from 3lufA/T0634-3lufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lufA in template set Warning: unaligning (T0634)Y125 because last residue in template chain is (3lufA)Q246 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHH 3lufA 123 :IEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQH T0634 46 :HPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 3lufA 167 :AIRLVLVDYYMPEIDGISLVRMLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHNLEALE Number of specific fragments extracted= 2 number of extra gaps= 0 total=12 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gt7A/T0634-3gt7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gt7A expands to /projects/compbio/data/pdb/3gt7.pdb.gz 3gt7A:Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 3gt7A # T0634 read from 3gt7A/T0634-3gt7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gt7A read from 3gt7A/T0634-3gt7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gt7A to template set # found chain 3gt7A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3gt7A)A11 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3gt7A)P115 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3gt7A)P115 Warning: unaligning (T0634)Y126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3gt7A)E142 Warning: unaligning (T0634)S127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3gt7A)E142 Warning: unaligning (T0634)H139 because last residue in template chain is (3gt7A)F148 T0634 4 :KKILIIDQQDFSRIELKNFLD 3gt7A 12 :GEILIVEDSPTQAEHLKHILE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLT 3gt7A 34 :TGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFIT T0634 107 :FNRNDLLSRIEIHLRTQNY 3gt7A 116 :CKDVVLASHVKRLLSGVKR T0634 134 :GHHHH 3gt7A 143 :SITLA Number of specific fragments extracted= 4 number of extra gaps= 2 total=16 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gt7A/T0634-3gt7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3gt7A/T0634-3gt7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gt7A read from 3gt7A/T0634-3gt7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gt7A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3gt7A)A11 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3gt7A)P115 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3gt7A)P115 Warning: unaligning (T0634)Y126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3gt7A)E142 Warning: unaligning (T0634)S127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3gt7A)E142 Warning: unaligning (T0634)H139 because last residue in template chain is (3gt7A)F148 T0634 4 :KKILIIDQQ 3gt7A 12 :GEILIVEDS T0634 13 :DFSRI 3gt7A 22 :TQAEH T0634 19 :LKNFLDSE 3gt7A 27 :LKHILEET T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3gt7A 36 :YQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILL T0634 84 :SSEHKEA 3gt7A 92 :TILSDPR T0634 91 :IVNGLHSGADDYLT 3gt7A 100 :VVRSLECGADDFIT T0634 107 :FNRNDLLSRIEIHLRTQNY 3gt7A 116 :CKDVVLASHVKRLLSGVKR T0634 134 :GHHHH 3gt7A 143 :SITLA Number of specific fragments extracted= 8 number of extra gaps= 2 total=24 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gt7A/T0634-3gt7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3gt7A/T0634-3gt7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gt7A read from 3gt7A/T0634-3gt7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gt7A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3gt7A)A11 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3gt7A)P115 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3gt7A)P115 Warning: unaligning (T0634)Y126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3gt7A)E142 Warning: unaligning (T0634)S127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3gt7A)E142 Warning: unaligning (T0634)H139 because last residue in template chain is (3gt7A)F148 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLT 3gt7A 12 :GEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFIT T0634 107 :FNRNDLLSRIEIHLRTQNY 3gt7A 116 :CKDVVLASHVKRLLSGVKR T0634 134 :GHHHH 3gt7A 143 :SITLA Number of specific fragments extracted= 3 number of extra gaps= 2 total=27 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3f6pA/T0634-3f6pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3f6pA expands to /projects/compbio/data/pdb/3f6p.pdb.gz 3f6pA:# T0634 read from 3f6pA/T0634-3f6pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f6pA read from 3f6pA/T0634-3f6pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3f6pA to template set # found chain 3f6pA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3f6pA)M1 T0634 3 :LKKILIIDQQDFSRIELKNFLD 3f6pA 2 :DKKILVVDDEKPIADILEFNLR T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKR 3f6pA 25 :EGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRK T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 3f6pA 71 :KYDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLR Number of specific fragments extracted= 3 number of extra gaps= 0 total=30 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3f6pA/T0634-3f6pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3f6pA/T0634-3f6pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f6pA read from 3f6pA/T0634-3f6pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3f6pA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3f6pA)M1 T0634 3 :LKKILIIDQQ 3f6pA 2 :DKKILVVDDE T0634 13 :DFSRI 3f6pA 13 :PIADI T0634 19 :LKNFLDSE 3f6pA 18 :LEFNLRKE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 3f6pA 27 :YEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKK T0634 75 :KNVPLILL 3f6pA 72 :YDMPIIML T0634 84 :SSEHKEA 3f6pA 80 :TAKDSEI T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRT 3f6pA 88 :KVIGLEIGADDYVTKPFSTRELLARVKANLRR Number of specific fragments extracted= 7 number of extra gaps= 0 total=37 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3f6pA/T0634-3f6pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3f6pA/T0634-3f6pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f6pA read from 3f6pA/T0634-3f6pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3f6pA in template set T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 3f6pA 1 :MDKKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKK T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 3f6pA 72 :YDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLR Number of specific fragments extracted= 2 number of extra gaps= 0 total=39 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oqrA/T0634-2oqrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2oqrA expands to /projects/compbio/data/pdb/2oqr.pdb.gz 2oqrA:Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2oqrA # T0634 read from 2oqrA/T0634-2oqrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oqrA read from 2oqrA/T0634-2oqrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2oqrA to template set # found chain 2oqrA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2oqrA)A1 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2oqrA)P102 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2oqrA)P102 T0634 4 :KKILIIDQQDFSRIELKNFLD 2oqrA 2 :TSVLIVEDEESLADPLAFLLR T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2oqrA 24 :EGFEATVVTDGPAALAEFDRAGADIVLLDLMLPGMSGTDVCKQLRAR T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLT 2oqrA 71 :SSVPVIMVTARDSEIDKVVGLELGADDYVT T0634 107 :FNRNDLLSRIEIHLRTQNYYSD 2oqrA 103 :YSARELIARIRAVLRRGGDDDS T0634 130 :RKNEGH 2oqrA 127 :SDGVLE Number of specific fragments extracted= 5 number of extra gaps= 1 total=44 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oqrA/T0634-2oqrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2oqrA/T0634-2oqrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oqrA read from 2oqrA/T0634-2oqrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oqrA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2oqrA)A1 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2oqrA)P102 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2oqrA)P102 T0634 4 :KKILIIDQQ 2oqrA 2 :TSVLIVEDE T0634 13 :DFSRI 2oqrA 12 :SLADP T0634 19 :LKNFLDSE 2oqrA 17 :LAFLLRKE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2oqrA 26 :FEATVVTDGPAALAEFDRAGADIVLLDLMLPGMSGTDVCKQLRAR T0634 75 :KNVPLILL 2oqrA 71 :SSVPVIMV T0634 84 :SSEHKEA 2oqrA 79 :TARDSEI T0634 91 :IVNGLHSGADDYLT 2oqrA 87 :KVVGLELGADDYVT T0634 107 :FNRNDLLSRIEIHLRTQNYYSDLRKNE 2oqrA 103 :YSARELIARIRAVLRRGGDDDSEMSDG Number of specific fragments extracted= 8 number of extra gaps= 1 total=52 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oqrA/T0634-2oqrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2oqrA/T0634-2oqrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oqrA read from 2oqrA/T0634-2oqrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oqrA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (2oqrA)A1 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2oqrA)P102 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2oqrA)P102 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2oqrA 2 :TSVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFDRAGADIVLLDLMLPGMSGTDVCKQLRAR T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLT 2oqrA 71 :SSVPVIMVTARDSEIDKVVGLELGADDYVT T0634 107 :FNRNDLLSRIEIHLRTQNYY 2oqrA 103 :YSARELIARIRAVLRRGGDD Number of specific fragments extracted= 3 number of extra gaps= 1 total=55 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3khtA/T0634-3khtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3khtA expands to /projects/compbio/data/pdb/3kht.pdb.gz 3khtA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 3khtA/T0634-3khtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3khtA read from 3khtA/T0634-3khtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3khtA to template set # found chain 3khtA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3khtA)S14 Warning: unaligning (T0634)R130 because last residue in template chain is (3khtA)Q145 T0634 4 :KKILIIDQQDFSRIELKNFLD 3khtA 15 :KRVLVVEDNPDDIALIRRVLD T0634 25 :SEY 3khtA 37 :KDI T0634 28 :LVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTK 3khtA 42 :QLEFVDNGAKALYQVQQAKYDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVDK T0634 106 :PFNRNDLLSRIEIHLRTQNYYSDL 3khtA 121 :SNNVTDFYGRIYAIFSYWLTVNHC Number of specific fragments extracted= 4 number of extra gaps= 0 total=59 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3khtA/T0634-3khtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3khtA/T0634-3khtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3khtA read from 3khtA/T0634-3khtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3khtA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3khtA)S14 Warning: unaligning (T0634)R130 because last residue in template chain is (3khtA)Q145 T0634 4 :KKILIIDQQ 3khtA 15 :KRVLVVEDN T0634 13 :DFSRI 3khtA 25 :DDIAL T0634 19 :LKNFLDSE 3khtA 30 :IRRVLDRK T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3khtA 41 :CQLEFVDNGAKALYQVQQAKYDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVIL T0634 84 :SSEHKEA 3khtA 97 :TDNVSDD T0634 91 :IVNGLHSGADDYLTKPF 3khtA 105 :AKQCMAAGASSVVDKSS T0634 108 :NRNDLLSRIEIHLRTQNYYSDL 3khtA 123 :NVTDFYGRIYAIFSYWLTVNHC Number of specific fragments extracted= 7 number of extra gaps= 0 total=66 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3khtA/T0634-3khtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3khtA/T0634-3khtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3khtA read from 3khtA/T0634-3khtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3khtA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3khtA)S14 Warning: unaligning (T0634)H136 because last residue in template chain is (3khtA)Q145 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEY 3khtA 15 :KRVLVVEDNPDDIALIRRVLDRKDI T0634 28 :LVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 3khtA 42 :QLEFVDNGAKALYQVQQAKYDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVDKSSNNVTDFYGRIYAIFSY T0634 129 :LRKNEGH 3khtA 138 :WLTVNHC Number of specific fragments extracted= 3 number of extra gaps= 0 total=69 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cg4A/T0634-3cg4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cg4A expands to /projects/compbio/data/pdb/3cg4.pdb.gz 3cg4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 172, because occupancy 0.300 <= existing 0.700 in 3cg4A Skipped atom 174, because occupancy 0.350 <= existing 0.350 in 3cg4A Skipped atom 175, because occupancy 0.300 <= existing 0.350 in 3cg4A Skipped atom 177, because occupancy 0.300 <= existing 0.700 in 3cg4A Skipped atom 179, because occupancy 0.300 <= existing 0.700 in 3cg4A Skipped atom 181, because occupancy 0.350 <= existing 0.350 in 3cg4A Skipped atom 182, because occupancy 0.300 <= existing 0.350 in 3cg4A Skipped atom 184, because occupancy 0.350 <= existing 0.350 in 3cg4A Skipped atom 185, because occupancy 0.300 <= existing 0.350 in 3cg4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 3cg4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 3cg4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 3cg4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 3cg4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 3cg4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 3cg4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 3cg4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 3cg4A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 3cg4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 3cg4A/T0634-3cg4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cg4A read from 3cg4A/T0634-3cg4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cg4A to template set # found chain 3cg4A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3cg4A)H4 Warning: unaligning (T0634)E86 because of BadResidue code BAD_PEPTIDE in next template residue (3cg4A)A90 Warning: unaligning (T0634)H87 because of BadResidue code BAD_PEPTIDE at template residue (3cg4A)A90 Warning: unaligning (T0634)Y126 because last residue in template chain is (3cg4A)Q129 T0634 3 :LKKILIIDQQDFSRIELKNFLD 3cg4A 5 :KGDVMIVDDDAHVRIAVKTILS T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSS 3cg4A 28 :AGFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIVMLTAK T0634 88 :KEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNY 3cg4A 91 :PDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMGFVRN Number of specific fragments extracted= 3 number of extra gaps= 1 total=72 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cg4A/T0634-3cg4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3cg4A/T0634-3cg4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cg4A read from 3cg4A/T0634-3cg4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cg4A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3cg4A)H4 Warning: unaligning (T0634)H87 because of BadResidue code BAD_PEPTIDE in next template residue (3cg4A)A90 Warning: unaligning (T0634)K88 because of BadResidue code BAD_PEPTIDE at template residue (3cg4A)A90 Warning: unaligning (T0634)Y126 because last residue in template chain is (3cg4A)Q129 T0634 3 :LKKILIIDQQ 3cg4A 5 :KGDVMIVDDD T0634 13 :DFSRI 3cg4A 16 :HVRIA T0634 19 :LKNFLDSE 3cg4A 21 :VKTILSDA T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3cg4A 30 :FHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIVML T0634 84 :SSE 3cg4A 86 :TAK T0634 89 :EA 3cg4A 91 :PD T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNY 3cg4A 94 :KMIGLQEYVVDYITKPFDNEDLIEKTTFFMGFVRN Number of specific fragments extracted= 7 number of extra gaps= 1 total=79 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cg4A/T0634-3cg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3cg4A/T0634-3cg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cg4A read from 3cg4A/T0634-3cg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cg4A in template set Warning: unaligning (T0634)E86 because of BadResidue code BAD_PEPTIDE in next template residue (3cg4A)A90 Warning: unaligning (T0634)H87 because of BadResidue code BAD_PEPTIDE at template residue (3cg4A)A90 Warning: unaligning (T0634)Y126 because last residue in template chain is (3cg4A)Q129 T0634 2 :SLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSS 3cg4A 5 :KGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIVMLTAK T0634 88 :KEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNY 3cg4A 91 :PDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMGFVRN Number of specific fragments extracted= 2 number of extra gaps= 1 total=81 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2zwmA/T0634-2zwmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2zwmA expands to /projects/compbio/data/pdb/2zwm.pdb.gz 2zwmA:# T0634 read from 2zwmA/T0634-2zwmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2zwmA read from 2zwmA/T0634-2zwmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2zwmA to template set # found chain 2zwmA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2zwmA)D1 Warning: unaligning (T0634)N124 because last residue in template chain is (2zwmA)L120 T0634 4 :KKILIIDQQDFSRIELKNFLD 2zwmA 2 :KKILVVDDEKPIADILEFNLR T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2zwmA 24 :EGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKK T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 2zwmA 71 :YDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLRRQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=84 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2zwmA/T0634-2zwmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2zwmA/T0634-2zwmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2zwmA read from 2zwmA/T0634-2zwmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2zwmA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2zwmA)D1 Warning: unaligning (T0634)N124 because last residue in template chain is (2zwmA)L120 T0634 4 :KKILIIDQQ 2zwmA 2 :KKILVVDDE T0634 13 :DFSRI 2zwmA 12 :PIADI T0634 19 :LKNFLDSE 2zwmA 17 :LEFNLRKE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2zwmA 26 :YEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKK T0634 75 :KNVPLILL 2zwmA 71 :YDMPIIML T0634 84 :SSEHKEA 2zwmA 79 :TAKDSEI T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 2zwmA 87 :KVIGLEIGADDYVTKPFSTRELLARVKANLRRQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=91 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2zwmA/T0634-2zwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2zwmA/T0634-2zwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2zwmA read from 2zwmA/T0634-2zwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2zwmA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (2zwmA)D1 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2zwmA 2 :KKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKK T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRT 2zwmA 71 :YDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLRR Number of specific fragments extracted= 2 number of extra gaps= 0 total=93 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kgsA/T0634-1kgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kgsA expands to /projects/compbio/data/pdb/1kgs.pdb.gz 1kgsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 1kgsA Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 1kgsA Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 1kgsA Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 1kgsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 1kgsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 1kgsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 1kgsA Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 1kgsA Skipped atom 393, because occupancy 0.500 <= existing 0.500 in 1kgsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 1kgsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1kgsA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 1kgsA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1kgsA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1kgsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1322, because occupancy 0.500 <= existing 0.500 in 1kgsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1324, because occupancy 0.500 <= existing 0.500 in 1kgsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1326, because occupancy 0.500 <= existing 0.500 in 1kgsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1328, because occupancy 0.500 <= existing 0.500 in 1kgsA # T0634 read from 1kgsA/T0634-1kgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kgsA read from 1kgsA/T0634-1kgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kgsA to template set # found chain 1kgsA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1kgsA)N2 T0634 4 :KKILIIDQQDFSRIELKNFLD 1kgsA 3 :VRVLVVEDERDLADLITEALK T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1kgsA 25 :EMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMRES T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNY 1kgsA 72 :GVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRKSE Number of specific fragments extracted= 3 number of extra gaps= 0 total=96 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kgsA/T0634-1kgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1kgsA/T0634-1kgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kgsA read from 1kgsA/T0634-1kgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kgsA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1kgsA)N2 T0634 4 :KKILIIDQQ 1kgsA 3 :VRVLVVEDE T0634 13 :DFSRI 1kgsA 13 :DLADL T0634 19 :LKNFLDSE 1kgsA 18 :ITEALKKE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1kgsA 27 :FTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMRESG T0634 75 :KNVPLILL 1kgsA 73 :VNTPVLML T0634 84 :SSEHKEA 1kgsA 81 :TALSDVE T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYS 1kgsA 89 :RVKGLNMGADDYLPKPFDLRELIARVRALIRRKSESK Number of specific fragments extracted= 7 number of extra gaps= 0 total=103 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kgsA/T0634-1kgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1kgsA/T0634-1kgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kgsA read from 1kgsA/T0634-1kgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kgsA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1kgsA)N2 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1kgsA 3 :VRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMRESG T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 1kgsA 73 :VNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRK Number of specific fragments extracted= 2 number of extra gaps= 0 total=105 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qzjA/T0634-2qzjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qzjA expands to /projects/compbio/data/pdb/2qzj.pdb.gz 2qzjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 2qzjA/T0634-2qzjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qzjA read from 2qzjA/T0634-2qzjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qzjA to template set # found chain 2qzjA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2qzjA)Q4 Warning: unaligning (T0634)Y125 because last residue in template chain is (2qzjA)S124 T0634 4 :KKILIIDQQDFSRIELKNFLD 2qzjA 5 :TKILIIDGDKDNCQKLKGFLE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2qzjA 27 :KGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNV T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 2qzjA 74 :TTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMN Number of specific fragments extracted= 3 number of extra gaps= 0 total=108 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qzjA/T0634-2qzjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2qzjA/T0634-2qzjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qzjA read from 2qzjA/T0634-2qzjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qzjA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2qzjA)Q4 Warning: unaligning (T0634)Y125 because last residue in template chain is (2qzjA)S124 T0634 4 :KKILIIDQQ 2qzjA 5 :TKILIIDGD T0634 13 :DFSRI 2qzjA 15 :DNCQK T0634 19 :LKNFLDSE 2qzjA 20 :LKGFLEEK T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2qzjA 29 :ISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNV T0634 75 :KNVPLILL 2qzjA 74 :TTCPIVYM T0634 84 :SSEHKEA 2qzjA 82 :TYINEDQ T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 2qzjA 90 :ILNALNSGGDDYLIKPLNLEILYAKVKAILRRMN Number of specific fragments extracted= 7 number of extra gaps= 0 total=115 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qzjA/T0634-2qzjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2qzjA/T0634-2qzjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qzjA read from 2qzjA/T0634-2qzjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qzjA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (2qzjA)Q4 Warning: unaligning (T0634)Y125 because last residue in template chain is (2qzjA)S124 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2qzjA 5 :TKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNV T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 2qzjA 74 :TTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMN Number of specific fragments extracted= 2 number of extra gaps= 0 total=117 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u8tA/T0634-1u8tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u8tA expands to /projects/compbio/data/pdb/1u8t.pdb.gz 1u8tA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 1u8tA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 1u8tA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 1u8tA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 1u8tA/T0634-1u8tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u8tA read from 1u8tA/T0634-1u8tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u8tA to template set # found chain 1u8tA in template set Warning: unaligning (T0634)T122 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1u8tA)M129 T0634 1 :MSLKKILIIDQQDFSRIELKNFLD 1u8tA 3 :DKELKFLVVDKFSTMRRIVRNLLK T0634 25 :SEY 1u8tA 28 :LGF T0634 28 :LVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 1u8tA 32 :NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGWVVKPFTAATLEEKLNKIFE Number of specific fragments extracted= 3 number of extra gaps= 0 total=120 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u8tA/T0634-1u8tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1u8tA/T0634-1u8tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u8tA read from 1u8tA/T0634-1u8tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u8tA in template set Warning: unaligning (T0634)T122 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1u8tA)M129 T0634 3 :LKKILIIDQQ 1u8tA 5 :ELKFLVVDKF T0634 13 :DFSRI 1u8tA 16 :TMRRI T0634 19 :LKNFLDSE 1u8tA 21 :VRNLLKEL T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 1u8tA 31 :NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMV T0634 84 :SSEHKEA 1u8tA 87 :TAEAKKE T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 1u8tA 95 :IIAAAQAGASGWVVKPFTAATLEEKLNKIFE Number of specific fragments extracted= 6 number of extra gaps= 0 total=126 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u8tA/T0634-1u8tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1u8tA/T0634-1u8tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u8tA read from 1u8tA/T0634-1u8tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u8tA in template set Warning: unaligning (T0634)T122 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1u8tA)M129 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEY 1u8tA 6 :LKFLVVDKFSTMRRIVRNLLKELGF T0634 28 :LVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 1u8tA 32 :NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGWVVKPFTAATLEEKLNKIFE Number of specific fragments extracted= 2 number of extra gaps= 0 total=128 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2zayA/T0634-2zayA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2zayA expands to /projects/compbio/data/pdb/2zay.pdb.gz 2zayA:# T0634 read from 2zayA/T0634-2zayA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2zayA read from 2zayA/T0634-2zayA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2zayA to template set # found chain 2zayA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2zayA)W8 Warning: unaligning (T0634)N124 because last residue in template chain is (2zayA)Y130 T0634 4 :KKILIIDQQDFSRIELKNFLD 2zayA 9 :WRIMLVDTQLPALAASISALS T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 2zayA 31 :EGFDIIQCGNAIEAVPVAVKTHPHLIITEANMPKISGMDLFNSLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRVLKLL Number of specific fragments extracted= 2 number of extra gaps= 0 total=130 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2zayA/T0634-2zayA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2zayA/T0634-2zayA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2zayA read from 2zayA/T0634-2zayA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2zayA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2zayA)W8 Warning: unaligning (T0634)N124 because last residue in template chain is (2zayA)Y130 T0634 4 :KKILIIDQQ 2zayA 9 :WRIMLVDTQ T0634 13 :DFSRI 2zayA 19 :PALAA T0634 19 :LKNFLDSE 2zayA 24 :SISALSQE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 2zayA 33 :FDIIQCGNAIEAVPVAVKTHPHLIITEANMPKISGMDLFNSLKKNPQTASIPVIAL T0634 84 :SSEHKEA 2zayA 89 :SGRATAK T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 2zayA 97 :EAQLLDMGFIDFIAKPVNAIRLSARIKRVLKLL Number of specific fragments extracted= 6 number of extra gaps= 0 total=136 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2zayA/T0634-2zayA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2zayA/T0634-2zayA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2zayA read from 2zayA/T0634-2zayA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2zayA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (2zayA)W8 Warning: unaligning (T0634)N124 because last residue in template chain is (2zayA)Y130 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 2zayA 9 :WRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAVKTHPHLIITEANMPKISGMDLFNSLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRVLKLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=137 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yioA/T0634-1yioA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yioA expands to /projects/compbio/data/pdb/1yio.pdb.gz 1yioA:Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 1yioA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 1yioA # T0634 read from 1yioA/T0634-1yioA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yioA read from 1yioA/T0634-1yioA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yioA to template set # found chain 1yioA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1yioA)A3 Warning: unaligning (T0634)Y27 because of BadResidue code BAD_PEPTIDE in next template residue (1yioA)E30 Warning: unaligning (T0634)L28 because of BadResidue code BAD_PEPTIDE at template residue (1yioA)E30 T0634 3 :LKKILIIDQQDFSRIELKNFLD 1yioA 4 :KPTVFVVDDDMSVREGLRNLLR T0634 25 :SE 1yioA 27 :AG T0634 29 :VIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1yioA 31 :VETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQEQLTAI T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYS 1yioA 74 :SDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNAERR Number of specific fragments extracted= 4 number of extra gaps= 1 total=141 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yioA/T0634-1yioA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1yioA/T0634-1yioA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yioA read from 1yioA/T0634-1yioA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yioA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1yioA)A3 Warning: unaligning (T0634)Y27 because of BadResidue code BAD_PEPTIDE in next template residue (1yioA)E30 Warning: unaligning (T0634)L28 because of BadResidue code BAD_PEPTIDE at template residue (1yioA)E30 T0634 3 :LKKILIIDQQ 1yioA 4 :KPTVFVVDDD T0634 13 :DFSRI 1yioA 15 :SVREG T0634 19 :LKNFLDSE 1yioA 20 :LRNLLRSA T0634 29 :VIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1yioA 31 :VETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQEQLTAIS T0634 75 :KNVPLILL 1yioA 75 :DGIPIVFI T0634 84 :SSEHKEA 1yioA 83 :TAHGDIP T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNY 1yioA 91 :TVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNAE Number of specific fragments extracted= 7 number of extra gaps= 1 total=148 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yioA/T0634-1yioA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1yioA/T0634-1yioA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yioA read from 1yioA/T0634-1yioA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yioA in template set Warning: unaligning (T0634)Y27 because of BadResidue code BAD_PEPTIDE in next template residue (1yioA)E30 Warning: unaligning (T0634)L28 because of BadResidue code BAD_PEPTIDE at template residue (1yioA)E30 T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSE 1yioA 3 :AKPTVFVVDDDMSVREGLRNLLRSAG T0634 29 :VIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1yioA 31 :VETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQEQLTAIS T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRK 1yioA 75 :DGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNAERRQARE Number of specific fragments extracted= 3 number of extra gaps= 1 total=151 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zgzA/T0634-1zgzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zgzA expands to /projects/compbio/data/pdb/1zgz.pdb.gz 1zgzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 1zgzA/T0634-1zgzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zgzA read from 1zgzA/T0634-1zgzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zgzA to template set # found chain 1zgzA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1zgzA)P2 Warning: unaligning (T0634)L74 because of BadResidue code BAD_PEPTIDE in next template residue (1zgzA)S72 Warning: unaligning (T0634)K75 because of BadResidue code BAD_PEPTIDE at template residue (1zgzA)S72 T0634 4 :KKILIIDQQDFSRIELKNFLD 1zgzA 3 :HHIVIVEDEPVTQARLQSYFT T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKR 1zgzA 25 :EGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRE T0634 76 :NVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 1zgzA 73 :TVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRID Number of specific fragments extracted= 3 number of extra gaps= 1 total=154 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zgzA/T0634-1zgzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1zgzA/T0634-1zgzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zgzA read from 1zgzA/T0634-1zgzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zgzA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1zgzA)P2 Warning: unaligning (T0634)S71 because of BadResidue code BAD_PEPTIDE in next template residue (1zgzA)S72 Warning: unaligning (T0634)K75 because of BadResidue code BAD_PEPTIDE at template residue (1zgzA)S72 T0634 4 :KKILIIDQQ 1zgzA 3 :HHIVIVEDE T0634 13 :DFSRI 1zgzA 13 :VTQAR T0634 19 :LKNFLDSE 1zgzA 18 :LQSYFTQE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKR 1zgzA 27 :YTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRE T0634 76 :NVPLILL 1zgzA 73 :TVGIILV T0634 84 :SSEHKEA 1zgzA 80 :TGRSDRI T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 1zgzA 88 :RIVGLEMGADDYVTKPLELRELVVRVKNLLWRID Number of specific fragments extracted= 7 number of extra gaps= 1 total=161 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zgzA/T0634-1zgzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1zgzA/T0634-1zgzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zgzA read from 1zgzA/T0634-1zgzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zgzA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1zgzA)P2 Warning: unaligning (T0634)S71 because of BadResidue code BAD_PEPTIDE in next template residue (1zgzA)S72 Warning: unaligning (T0634)K75 because of BadResidue code BAD_PEPTIDE at template residue (1zgzA)S72 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKR 1zgzA 3 :HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRE T0634 76 :NVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 1zgzA 73 :TVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRID Number of specific fragments extracted= 2 number of extra gaps= 1 total=163 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3grcA/T0634-3grcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3grcA expands to /projects/compbio/data/pdb/3grc.pdb.gz 3grcA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 3grcA/T0634-3grcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3grcA read from 3grcA/T0634-3grcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3grcA to template set # found chain 3grcA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3grcA)P546 Warning: unaligning (T0634)N124 because last residue in template chain is (3grcA)A670 T0634 3 :LKKILIIDQQDFSRIELKNFLD 3grcA 547 :RPRILICEDDPDIARLLNLMLE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVN 3grcA 570 :GGFDSDMVHSAAQALEQVARRPYAAMTVDLNLPDQDGVSLIRALRRDSRTRDLAIVVVSANAREGELEF T0634 96 :HSGADDYLTKPFNRNDLLSRIEIHLRTQ 3grcA 642 :PLAVSTWLEKPIDENLLILSLHRAIDNM Number of specific fragments extracted= 3 number of extra gaps= 0 total=166 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3grcA/T0634-3grcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3grcA/T0634-3grcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3grcA read from 3grcA/T0634-3grcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3grcA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3grcA)P546 Warning: unaligning (T0634)N124 because last residue in template chain is (3grcA)A670 T0634 3 :LKKILIIDQQ 3grcA 547 :RPRILICEDD T0634 13 :DFSRI 3grcA 558 :DIARL T0634 19 :LKNFLDSE 3grcA 563 :LNLMLEKG T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3grcA 572 :FDSDMVHSAAQALEQVARRPYAAMTVDLNLPDQDGVSLIRALRRDSRTRDLAIVVV T0634 84 :SSEHKEA 3grcA 628 :SANAREG T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 3grcA 637 :EFNSQPLAVSTWLEKPIDENLLILSLHRAIDNM Number of specific fragments extracted= 6 number of extra gaps= 0 total=172 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3grcA/T0634-3grcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3grcA/T0634-3grcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3grcA read from 3grcA/T0634-3grcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3grcA in template set Warning: unaligning (T0634)N124 because last residue in template chain is (3grcA)A670 T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLF 3grcA 546 :PRPRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVARRPYAAMTVDLNLPDQDGVSLIRALRRDSRTRDLAIVVVS T0634 85 :SEHKEAIVNGL 3grcA 629 :ANAREGELEFN T0634 96 :HSGADDYLTKPFNRNDLLSRIEIHLRTQ 3grcA 642 :PLAVSTWLEKPIDENLLILSLHRAIDNM Number of specific fragments extracted= 3 number of extra gaps= 0 total=175 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dgfC/T0634-3dgfC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3dgfC expands to /projects/compbio/data/pdb/3dgf.pdb.gz 3dgfC:Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 3dgfC # T0634 read from 3dgfC/T0634-3dgfC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dgfC read from 3dgfC/T0634-3dgfC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dgfC to template set # found chain 3dgfC in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3dgfC)S2 Warning: unaligning (T0634)H96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dgfC)L97 Warning: unaligning (T0634)S97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)L97 Warning: unaligning (T0634)G98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dgfC)A99 Warning: unaligning (T0634)A99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)A99 Warning: unaligning (T0634)D100 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)R100 Warning: unaligning (T0634)D101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)K101 Warning: unaligning (T0634)T104 because of BadResidue code BAD_PEPTIDE in next template residue (3dgfC)K105 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE at template residue (3dgfC)K105 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE at template residue (3dgfC)P106 T0634 4 :KKILIIDQQDFSRIELKNFLD 3dgfC 3 :KKVLLVDDSAVLRKIVSFNLK T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGL 3dgfC 25 :EGYEVIEAENGQIALEKLSEFTPDLIVLDIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLAL T0634 102 :YL 3dgfC 102 :VM T0634 107 :FNRNDLLSRIEIHL 3dgfC 107 :FSPSQFIEEVKHLL Number of specific fragments extracted= 4 number of extra gaps= 2 total=179 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dgfC/T0634-3dgfC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3dgfC/T0634-3dgfC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dgfC read from 3dgfC/T0634-3dgfC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dgfC in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3dgfC)S2 Warning: unaligning (T0634)H96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dgfC)L97 Warning: unaligning (T0634)S97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)L97 Warning: unaligning (T0634)G98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dgfC)A99 Warning: unaligning (T0634)A99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)A99 Warning: unaligning (T0634)D100 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)R100 Warning: unaligning (T0634)D101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)K101 Warning: unaligning (T0634)T104 because of BadResidue code BAD_PEPTIDE in next template residue (3dgfC)K105 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE at template residue (3dgfC)K105 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE at template residue (3dgfC)P106 T0634 4 :KKILIIDQQ 3dgfC 3 :KKVLLVDDS T0634 13 :DFSRI 3dgfC 13 :VLRKI T0634 19 :LKNFLDSE 3dgfC 18 :VSFNLKKE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3dgfC 27 :YEVIEAENGQIALEKLSEFTPDLIVLDIMMPVMDGFTVLKKLQEKEEWKRIPVIVL T0634 84 :SSEHKEA 3dgfC 83 :TAKGGEE T0634 91 :IVNGL 3dgfC 91 :ESLAL T0634 102 :YL 3dgfC 102 :VM T0634 107 :FNRNDLLSRIEIHL 3dgfC 107 :FSPSQFIEEVKHLL Number of specific fragments extracted= 8 number of extra gaps= 2 total=187 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dgfC/T0634-3dgfC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3dgfC/T0634-3dgfC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dgfC read from 3dgfC/T0634-3dgfC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dgfC in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3dgfC)S2 Warning: unaligning (T0634)H96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dgfC)L97 Warning: unaligning (T0634)S97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)L97 Warning: unaligning (T0634)G98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dgfC)A99 Warning: unaligning (T0634)A99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)A99 Warning: unaligning (T0634)D100 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)R100 Warning: unaligning (T0634)D101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)K101 Warning: unaligning (T0634)T104 because of BadResidue code BAD_PEPTIDE in next template residue (3dgfC)K105 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE at template residue (3dgfC)K105 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE at template residue (3dgfC)P106 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGL 3dgfC 3 :KKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLDIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLAL T0634 102 :YL 3dgfC 102 :VM T0634 107 :FNRNDLLSRIEIH 3dgfC 107 :FSPSQFIEEVKHL Number of specific fragments extracted= 3 number of extra gaps= 2 total=190 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zh2A/T0634-1zh2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zh2A expands to /projects/compbio/data/pdb/1zh2.pdb.gz 1zh2A:# T0634 read from 1zh2A/T0634-1zh2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zh2A read from 1zh2A/T0634-1zh2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zh2A to template set # found chain 1zh2A in template set Warning: unaligning (T0634)K4 because first residue in template chain is (1zh2A)T2 T0634 5 :KILIIDQQDFSRIELKNFLD 1zh2A 3 :NVLIVEDEQAIRRFLRTALE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKR 1zh2A 24 :DGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQ T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 1zh2A 70 :WSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHS Number of specific fragments extracted= 3 number of extra gaps= 0 total=193 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zh2A/T0634-1zh2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1zh2A/T0634-1zh2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zh2A read from 1zh2A/T0634-1zh2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zh2A in template set Warning: unaligning (T0634)K4 because first residue in template chain is (1zh2A)T2 T0634 5 :KILIIDQQ 1zh2A 3 :NVLIVEDE T0634 13 :DFSRI 1zh2A 12 :AIRRF T0634 19 :LKNFLDSE 1zh2A 17 :LRTALEGD T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1zh2A 26 :MRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQW T0634 75 :KNVPLILL 1zh2A 71 :SAVPVIVL T0634 84 :SSEHKEA 1zh2A 79 :SARSEES T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 1zh2A 87 :KIAALDAGADDYLSKPFGIGELQARLRVALRRHS Number of specific fragments extracted= 7 number of extra gaps= 0 total=200 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zh2A/T0634-1zh2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1zh2A/T0634-1zh2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zh2A read from 1zh2A/T0634-1zh2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zh2A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1zh2A)T2 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1zh2A 3 :NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQW T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 1zh2A 71 :SAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRH Number of specific fragments extracted= 2 number of extra gaps= 0 total=202 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gl9A/T0634-3gl9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gl9A expands to /projects/compbio/data/pdb/3gl9.pdb.gz 3gl9A:Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 3gl9A Bad short name: BE for alphabet: pdb_atoms Bad short name: F1 for alphabet: pdb_atoms Bad short name: F2 for alphabet: pdb_atoms Bad short name: F3 for alphabet: pdb_atoms Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 3gl9A # T0634 read from 3gl9A/T0634-3gl9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gl9A read from 3gl9A/T0634-3gl9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gl9A to template set # found chain 3gl9A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3gl9A)S2 Warning: unaligning (T0634)L52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3gl9A)I54 Warning: unaligning (T0634)M54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gl9A)I54 Warning: unaligning (T0634)R121 because last residue in template chain is (3gl9A)N121 T0634 4 :KKILIIDQQDFSRIELKNFLD 3gl9A 3 :KKVLLVDDSAVLRKIVSFNLK T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVI 3gl9A 25 :EGYEVIEAENGQIALEKLSEFTPDLIV T0634 55 :DIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3gl9A 55 :MMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLL Number of specific fragments extracted= 3 number of extra gaps= 0 total=205 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gl9A/T0634-3gl9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3gl9A/T0634-3gl9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gl9A read from 3gl9A/T0634-3gl9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gl9A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3gl9A)S2 Warning: unaligning (T0634)L52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3gl9A)I54 Warning: unaligning (T0634)M54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gl9A)I54 Warning: unaligning (T0634)R121 because last residue in template chain is (3gl9A)N121 T0634 4 :KKILIIDQQ 3gl9A 3 :KKVLLVDDS T0634 13 :DFSRI 3gl9A 13 :VLRKI T0634 19 :LKNFLDSE 3gl9A 18 :VSFNLKKE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVI 3gl9A 27 :YEVIEAENGQIALEKLSEFTPDLIV T0634 55 :DIIGENSPNLCLKLKRSKGLKNVPLILL 3gl9A 55 :MMPVMDGFTVLKKLQEKEEWKRIPVIVL T0634 84 :SSEHKEA 3gl9A 83 :TAKGGEE T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3gl9A 91 :ESLALSLGARKVMRKPFSPSQFIEEVKHLL Number of specific fragments extracted= 7 number of extra gaps= 0 total=212 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gl9A/T0634-3gl9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3gl9A/T0634-3gl9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gl9A read from 3gl9A/T0634-3gl9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gl9A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3gl9A)S2 Warning: unaligning (T0634)L52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3gl9A)I54 Warning: unaligning (T0634)M54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gl9A)I54 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVI 3gl9A 3 :KKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIV T0634 55 :DIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3gl9A 55 :MMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLL Number of specific fragments extracted= 2 number of extra gaps= 0 total=214 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a04A/T0634-1a04A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a04A expands to /projects/compbio/data/pdb/1a04.pdb.gz 1a04A:# T0634 read from 1a04A/T0634-1a04A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a04A read from 1a04A/T0634-1a04A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a04A to template set # found chain 1a04A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1a04A)E5 T0634 3 :LKKILIIDQQDFSRIELKNFLD 1a04A 6 :PATILLIDDHPMLRTGVKQLIS T0634 25 :SEYLVI 1a04A 30 :PDITVV T0634 31 :ESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1a04A 37 :EASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREK T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSD 1a04A 78 :SLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEMVLSE Number of specific fragments extracted= 4 number of extra gaps= 0 total=218 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a04A/T0634-1a04A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1a04A/T0634-1a04A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a04A read from 1a04A/T0634-1a04A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a04A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1a04A)E5 T0634 3 :LKKILIIDQQD 1a04A 6 :PATILLIDDHP T0634 14 :FSRI 1a04A 18 :LRTG T0634 19 :LKNFLDSE 1a04A 22 :VKQLISMA T0634 27 :YLVI 1a04A 32 :ITVV T0634 31 :ESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1a04A 37 :EASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKS T0634 75 :KNVPLILL 1a04A 79 :LSGRIVVF T0634 84 :SSEHKEA 1a04A 87 :SVSNHEE T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSD 1a04A 95 :VVTALKRGADGYLLKDMEPEDLLKALHQAAAGEMVLSE Number of specific fragments extracted= 8 number of extra gaps= 0 total=226 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a04A/T0634-1a04A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1a04A/T0634-1a04A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a04A read from 1a04A/T0634-1a04A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a04A in template set T0634 1 :MSLKKILIIDQQDFSRIELKNFLD 1a04A 5 :EPATILLIDDHPMLRTGVKQLISM T0634 25 :SEYLVI 1a04A 30 :PDITVV T0634 31 :ESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1a04A 37 :EASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREK T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 1a04A 78 :SLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAA Number of specific fragments extracted= 4 number of extra gaps= 0 total=230 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lteA/T0634-3lteA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lteA expands to /projects/compbio/data/pdb/3lte.pdb.gz 3lteA:# T0634 read from 3lteA/T0634-3lteA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lteA read from 3lteA/T0634-3lteA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lteA to template set # found chain 3lteA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3lteA)K68 T0634 5 :KILIIDQQDFSRIELKNFLD 3lteA 69 :RILVVDDDQAMAAAIERVLK T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEH 3lteA 90 :DHWQVEIAHNGFDAGIKLSTFEPAIMTLDLSMPKLDGLDVIRSLRQNKVANQPKILVVSGLDK T0634 89 :EAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3lteA 153 :AKLQQAVTEGADDYLEKPFDNDALLDRIHDLV Number of specific fragments extracted= 3 number of extra gaps= 0 total=233 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lteA/T0634-3lteA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3lteA/T0634-3lteA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lteA read from 3lteA/T0634-3lteA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lteA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3lteA)K68 T0634 5 :KILIIDQQ 3lteA 69 :RILVVDDD T0634 13 :DFSRI 3lteA 78 :AMAAA T0634 19 :LKNFLDSE 3lteA 83 :IERVLKRD T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3lteA 92 :WQVEIAHNGFDAGIKLSTFEPAIMTLDLSMPKLDGLDVIRSLRQNKVANQPKILVV T0634 84 :SSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3lteA 148 :SGLDKAKLQQAVTEGADDYLEKPFDNDALLDRIHDLV Number of specific fragments extracted= 5 number of extra gaps= 0 total=238 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lteA/T0634-3lteA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3lteA/T0634-3lteA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lteA read from 3lteA/T0634-3lteA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lteA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3lteA)K68 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 3lteA 69 :RILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKLSTFEPAIMTLDLSMPKLDGLDVIRSLRQNK T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3lteA 138 :VANQPKILVVSGLDKAKLQQAVTEGADDYLEKPFDNDALLDRIHDLV Number of specific fragments extracted= 2 number of extra gaps= 0 total=240 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2jbaA/T0634-2jbaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2jbaA expands to /projects/compbio/data/pdb/2jba.pdb.gz 2jbaA:Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 954, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 956, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2jbaA # T0634 read from 2jbaA/T0634-2jbaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jbaA read from 2jbaA/T0634-2jbaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2jbaA to template set # found chain 2jbaA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2jbaA)A2 T0634 4 :KKILIIDQQDFSRIELKNFLD 2jbaA 3 :RRILVVEDEAPIREMVCFVLE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 2jbaA 25 :NGFQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAVMRRIS Number of specific fragments extracted= 2 number of extra gaps= 0 total=242 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2jbaA/T0634-2jbaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2jbaA/T0634-2jbaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jbaA read from 2jbaA/T0634-2jbaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2jbaA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2jbaA)A2 T0634 4 :KKILIIDQQ 2jbaA 3 :RRILVVEDE T0634 13 :DFSRI 2jbaA 13 :PIREM T0634 19 :LKNFLDSE 2jbaA 18 :VCFVLEQN T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 2jbaA 27 :FQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVML T0634 84 :SSEHKEA 2jbaA 83 :TARGEEE T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNY 2jbaA 91 :RVRGLETGADDCITKPFSPKELVARIKAVMRRISP Number of specific fragments extracted= 6 number of extra gaps= 0 total=248 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2jbaA/T0634-2jbaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2jbaA/T0634-2jbaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jbaA read from 2jbaA/T0634-2jbaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2jbaA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (2jbaA)A2 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 2jbaA 3 :RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAVMR Number of specific fragments extracted= 1 number of extra gaps= 0 total=249 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xhfA/T0634-1xhfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xhfA expands to /projects/compbio/data/pdb/1xhf.pdb.gz 1xhfA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 1xhfA/T0634-1xhfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhfA read from 1xhfA/T0634-1xhfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xhfA to template set # found chain 1xhfA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1xhfA)Q2 T0634 3 :LKKILIIDQQDFSRIELKNFLD 1xhfA 3 :TPHILIVEDELVTRNTLKSIFE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1xhfA 26 :EGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQ T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 1xhfA 73 :ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRT Number of specific fragments extracted= 3 number of extra gaps= 0 total=252 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xhfA/T0634-1xhfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1xhfA/T0634-1xhfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhfA read from 1xhfA/T0634-1xhfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xhfA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1xhfA)Q2 T0634 3 :LKKILIIDQQD 1xhfA 3 :TPHILIVEDEL T0634 14 :FSRI 1xhfA 15 :TRNT T0634 19 :LKNFLDSE 1xhfA 19 :LKSIFEAE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1xhfA 28 :YDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQ T0634 75 :KNVPLILL 1xhfA 73 :ANVALMFL T0634 84 :SSEHKEA 1xhfA 81 :TGRDNEV T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 1xhfA 89 :KILGLEIGADDYITKPFNPRELTIRARNLLSRT Number of specific fragments extracted= 7 number of extra gaps= 0 total=259 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xhfA/T0634-1xhfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1xhfA/T0634-1xhfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhfA read from 1xhfA/T0634-1xhfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xhfA in template set T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1xhfA 2 :QTPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQ T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 1xhfA 73 :ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRT Number of specific fragments extracted= 2 number of extra gaps= 0 total=261 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cnbA/T0634-3cnbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cnbA expands to /projects/compbio/data/pdb/3cnb.pdb.gz 3cnbA:# T0634 read from 3cnbA/T0634-3cnbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cnbA read from 3cnbA/T0634-3cnbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cnbA to template set # found chain 3cnbA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3cnbA)F66 Warning: unaligning (T0634)E86 because of BadResidue code BAD_PEPTIDE in next template residue (3cnbA)T152 Warning: unaligning (T0634)H87 because of BadResidue code BAD_PEPTIDE at template residue (3cnbA)T152 Warning: unaligning (T0634)N124 because last residue in template chain is (3cnbA)K189 T0634 5 :KILIIDQQDFSRIELKNFLD 3cnbA 67 :SILIIEDDKEFADMLTQFLE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSS 3cnbA 90 :PYAKIKIAYNPFDAGDLLHTVKPDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAMTGA T0634 88 :KEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 3cnbA 153 :DDNVSRIVALGAETCFGKPLNFTLLEKTIKQLVEQK Number of specific fragments extracted= 3 number of extra gaps= 1 total=264 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cnbA/T0634-3cnbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3cnbA/T0634-3cnbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cnbA read from 3cnbA/T0634-3cnbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cnbA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3cnbA)F66 Warning: unaligning (T0634)H87 because of BadResidue code BAD_PEPTIDE in next template residue (3cnbA)T152 Warning: unaligning (T0634)K88 because of BadResidue code BAD_PEPTIDE at template residue (3cnbA)T152 Warning: unaligning (T0634)N124 because last residue in template chain is (3cnbA)K189 T0634 5 :KILIIDQQ 3cnbA 67 :SILIIEDD T0634 13 :DFSRI 3cnbA 76 :EFADM T0634 19 :LKNFLDSE 3cnbA 81 :LTQFLENL T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3cnbA 92 :AKIKIAYNPFDAGDLLHTVKPDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAM T0634 84 :SSE 3cnbA 148 :TGA T0634 89 :EA 3cnbA 153 :DD T0634 91 :IV 3cnbA 158 :RI T0634 95 :LHSGADDYLTKPFNRNDLLSRIEIHLRTQ 3cnbA 160 :VALGAETCFGKPLNFTLLEKTIKQLVEQK Number of specific fragments extracted= 8 number of extra gaps= 1 total=272 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cnbA/T0634-3cnbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3cnbA/T0634-3cnbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cnbA read from 3cnbA/T0634-3cnbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cnbA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3cnbA)F66 Warning: unaligning (T0634)E86 because of BadResidue code BAD_PEPTIDE in next template residue (3cnbA)T152 Warning: unaligning (T0634)H87 because of BadResidue code BAD_PEPTIDE at template residue (3cnbA)T152 Warning: unaligning (T0634)N124 because last residue in template chain is (3cnbA)K189 T0634 4 :KKILIIDQQDFSRIELKNFLD 3cnbA 67 :SILIIEDDKEFADMLTQFLEN T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSS 3cnbA 90 :PYAKIKIAYNPFDAGDLLHTVKPDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAMTGA T0634 88 :KEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 3cnbA 153 :DDNVSRIVALGAETCFGKPLNFTLLEKTIKQLVEQK Number of specific fragments extracted= 3 number of extra gaps= 1 total=275 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3crnA/T0634-3crnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3crnA expands to /projects/compbio/data/pdb/3crn.pdb.gz 3crnA:Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 164, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 168, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 170, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 172, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 3crnA Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 931, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 933, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 935, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 937, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 3crnA Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 3crnA # T0634 read from 3crnA/T0634-3crnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3crnA read from 3crnA/T0634-3crnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3crnA to template set # found chain 3crnA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3crnA)L1 Warning: unaligning (T0634)L52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3crnA)I53 Warning: unaligning (T0634)M54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3crnA)I53 T0634 4 :KKILIIDQQDFSRIELKNFLD 3crnA 2 :KRILIVDDDTAILDSTKQILE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVI 3crnA 24 :EGYEVEIAATAGEGLAKIENEFFNLAL T0634 55 :DIIGENSPNLCLKLKRS 3crnA 54 :KLPDMEGTELLEKAHKL T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 3crnA 71 :RPGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKLDEQEKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=279 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3crnA/T0634-3crnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3crnA/T0634-3crnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3crnA read from 3crnA/T0634-3crnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3crnA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3crnA)L1 Warning: unaligning (T0634)L52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3crnA)I53 Warning: unaligning (T0634)M54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3crnA)I53 T0634 4 :KKILIIDQQ 3crnA 2 :KRILIVDDD T0634 13 :DFSRI 3crnA 12 :AILDS T0634 19 :LKNFLDSE 3crnA 17 :TKQILEFE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVI 3crnA 26 :YEVEIAATAGEGLAKIENEFFNLAL T0634 55 :DIIGENSPNLCLKLKRS 3crnA 54 :KLPDMEGTELLEKAHKL T0634 74 :LKNVPLILL 3crnA 71 :RPGMKKIMV T0634 84 :SSEHKEA 3crnA 80 :TGYASLE T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 3crnA 88 :SVFSLNAGADAYIMKPVNPRDLLEKIKEKLDEQEKE Number of specific fragments extracted= 8 number of extra gaps= 0 total=287 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3crnA/T0634-3crnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3crnA/T0634-3crnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3crnA read from 3crnA/T0634-3crnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3crnA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3crnA)L1 Warning: unaligning (T0634)L52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3crnA)I53 Warning: unaligning (T0634)M54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3crnA)I53 Warning: unaligning (T0634)N132 because last residue in template chain is (3crnA)H129 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVI 3crnA 2 :KRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIENEFFNLAL T0634 55 :DIIGENSPNLCLKLKRS 3crnA 54 :KLPDMEGTELLEKAHKL T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRK 3crnA 71 :RPGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKLDEQEKEGHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=290 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3c3mA/T0634-3c3mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3c3mA expands to /projects/compbio/data/pdb/3c3m.pdb.gz 3c3mA:Skipped atom 3, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 7, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 426, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 428, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 430, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 432, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 436, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 454, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 3c3mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 690, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 692, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 3c3mA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 3c3mA # T0634 read from 3c3mA/T0634-3c3mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c3mA read from 3c3mA/T0634-3c3mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3c3mA to template set # found chain 3c3mA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3c3mA)S1 T0634 3 :LKKILIIDQQDFSRIELKNFLD 3c3mA 2 :LYTILVVDDSPMIVDVFVTMLE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIH 3c3mA 25 :GGYRPITAFSGEECLEALNATPPDLVLLDIMMEPMDGWETLERIKTDPATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHV Number of specific fragments extracted= 2 number of extra gaps= 0 total=292 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3c3mA/T0634-3c3mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3c3mA/T0634-3c3mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c3mA read from 3c3mA/T0634-3c3mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3c3mA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3c3mA)S1 T0634 3 :LKKILIIDQQD 3c3mA 2 :LYTILVVDDSP T0634 14 :FSRI 3c3mA 14 :IVDV T0634 19 :LKNFLDSE 3c3mA 18 :FVTMLERG T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3c3mA 27 :YRPITAFSGEECLEALNATPPDLVLLDIMMEPMDGWETLERIKTDPATRDIPVLML T0634 84 :SSEHKEA 3c3mA 83 :TAKPLTP T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3c3mA 91 :EANEYGSYIEDYILKPTTHHQLYEAIEHVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=298 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3c3mA/T0634-3c3mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3c3mA/T0634-3c3mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c3mA read from 3c3mA/T0634-3c3mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3c3mA in template set T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIH 3c3mA 1 :SLYTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALNATPPDLVLLDIMMEPMDGWETLERIKTDPATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHV Number of specific fragments extracted= 1 number of extra gaps= 0 total=299 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9oA/T0634-2a9oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a9oA expands to /projects/compbio/data/pdb/2a9o.pdb.gz 2a9oA:Skipped atom 224, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 228, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 856, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 916, because occupancy 0.500 <= existing 0.500 in 2a9oA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 2a9oA # T0634 read from 2a9oA/T0634-2a9oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a9oA read from 2a9oA/T0634-2a9oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a9oA to template set # found chain 2a9oA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (2a9oA)K2 Warning: unaligning (T0634)I51 because of BadResidue code BAD_PEPTIDE in next template residue (2a9oA)L51 Warning: unaligning (T0634)L52 because of BadResidue code BAD_PEPTIDE at template residue (2a9oA)L51 T0634 5 :KILIIDQQDFSRIELKNFLD 2a9oA 3 :KILIVDDEKPISDIIKFNMT T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLV 2a9oA 24 :EGYEVVTAFNGREALEQFEAEQPDII T0634 53 :DMDIIGENSPNLCLKLKRS 2a9oA 52 :DLMLPEIDGLEVAKTIRKT T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 2a9oA 71 :SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLR Number of specific fragments extracted= 4 number of extra gaps= 1 total=303 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9oA/T0634-2a9oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2a9oA/T0634-2a9oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a9oA read from 2a9oA/T0634-2a9oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a9oA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (2a9oA)K2 Warning: unaligning (T0634)I51 because of BadResidue code BAD_PEPTIDE in next template residue (2a9oA)L51 Warning: unaligning (T0634)L52 because of BadResidue code BAD_PEPTIDE at template residue (2a9oA)L51 T0634 5 :KILIIDQQ 2a9oA 3 :KILIVDDE T0634 13 :DFSRI 2a9oA 12 :PISDI T0634 19 :LKNFLDSE 2a9oA 17 :IKFNMTKE T0634 27 :YLVIESKNEKEALEQIDHHHPDLV 2a9oA 26 :YEVVTAFNGREALEQFEAEQPDII T0634 53 :DMDIIGENSPNLCLKLKRS 2a9oA 52 :DLMLPEIDGLEVAKTIRKT T0634 75 :KNVPLILL 2a9oA 71 :SSVPILML T0634 84 :SSEHKEA 2a9oA 79 :SAKDSEF T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 2a9oA 87 :KVIGLELGADDYVTKPFSNRELQARVKALLR Number of specific fragments extracted= 8 number of extra gaps= 1 total=311 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9oA/T0634-2a9oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2a9oA/T0634-2a9oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a9oA read from 2a9oA/T0634-2a9oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a9oA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2a9oA)K2 Warning: unaligning (T0634)I51 because of BadResidue code BAD_PEPTIDE in next template residue (2a9oA)L51 Warning: unaligning (T0634)L52 because of BadResidue code BAD_PEPTIDE at template residue (2a9oA)L51 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLV 2a9oA 3 :KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDII T0634 53 :DMDIIGENSPNLCLKLKRS 2a9oA 52 :DLMLPEIDGLEVAKTIRKT T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 2a9oA 71 :SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLR Number of specific fragments extracted= 3 number of extra gaps= 1 total=314 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cfyA/T0634-3cfyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cfyA expands to /projects/compbio/data/pdb/3cfy.pdb.gz 3cfyA:Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 3cfyA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 3cfyA # T0634 read from 3cfyA/T0634-3cfyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cfyA read from 3cfyA/T0634-3cfyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cfyA to template set # found chain 3cfyA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3cfyA)L1 T0634 3 :LKKILIIDQQDFSRIELKNFLD 3cfyA 2 :RPRVLLVEDSTSLAILYKQYVK T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 3cfyA 25 :EPYDIFHVETGRDAIQFIERSKPQLIILDLKLPDMSGEDVLDWINQN T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSD 3cfyA 72 :DIPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHLKRAKLEDL Number of specific fragments extracted= 3 number of extra gaps= 0 total=317 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cfyA/T0634-3cfyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3cfyA/T0634-3cfyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cfyA read from 3cfyA/T0634-3cfyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cfyA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3cfyA)L1 Warning: unaligning (T0634)N132 because last residue in template chain is (3cfyA)H130 T0634 3 :LKKILIIDQQ 3cfyA 2 :RPRVLLVEDS T0634 13 :DFSRI 3cfyA 13 :SLAIL T0634 19 :LKNFLDSE 3cfyA 18 :YKQYVKDE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 3cfyA 27 :YDIFHVETGRDAIQFIERSKPQLIILDLKLPDMSGEDVLDWINQND T0634 75 :KNVPLILL 3cfyA 73 :IPTSVIIA T0634 84 :SSEHKEAIVNGL 3cfyA 81 :TAHGSVDLAVNL T0634 96 :HSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRK 3cfyA 94 :QKGAEDFLEKPINADRLKTSVALHLKRAKLEDLVEG Number of specific fragments extracted= 7 number of extra gaps= 0 total=324 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cfyA/T0634-3cfyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3cfyA/T0634-3cfyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cfyA read from 3cfyA/T0634-3cfyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cfyA in template set Warning: unaligning (T0634)H136 because last residue in template chain is (3cfyA)H130 T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 3cfyA 1 :LRPRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIERSKPQLIILDLKLPDMSGEDVLDWINQND T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 3cfyA 73 :IPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHLKRAKLE T0634 131 :KNEGH 3cfyA 125 :DLVEG Number of specific fragments extracted= 3 number of extra gaps= 0 total=327 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hdgA/T0634-3hdgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hdgA expands to /projects/compbio/data/pdb/3hdg.pdb.gz 3hdgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 3hdgA/T0634-3hdgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hdgA read from 3hdgA/T0634-3hdgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hdgA to template set # found chain 3hdgA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3hdgA)A8 Warning: unaligning (T0634)S127 because last residue in template chain is (3hdgA)E131 T0634 4 :KKILIIDQQDFSRIELKNFLD 3hdgA 9 :LKILIVEDDTDAREWLSTIIS T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 3hdgA 31 :HFPEVWSAGDGEEGERLFGLHAPDVIITDIRMPKLGGLEMLDRIKAG T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 3hdgA 78 :GAKPYVIVISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFRHIKLAK Number of specific fragments extracted= 3 number of extra gaps= 0 total=330 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hdgA/T0634-3hdgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3hdgA/T0634-3hdgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hdgA read from 3hdgA/T0634-3hdgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hdgA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3hdgA)A8 Warning: unaligning (T0634)D128 because last residue in template chain is (3hdgA)E131 T0634 4 :KKILIIDQQ 3hdgA 9 :LKILIVEDD T0634 13 :DFSRI 3hdgA 19 :DAREW T0634 19 :LKNFLDSE 3hdgA 24 :LSTIISNH T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 3hdgA 33 :PEVWSAGDGEEGERLFGLHAPDVIITDIRMPKLGGLEMLDRIKAGG T0634 75 :KNVPLILL 3hdgA 79 :AKPYVIVI T0634 84 :SSEHKEA 3hdgA 87 :SAFSEMK T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 3hdgA 95 :FIKAIELGVHLFLPKPIEPGRLMETLEDFRH T0634 123 :QNYYS 3hdgA 126 :IKLAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=338 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hdgA/T0634-3hdgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3hdgA/T0634-3hdgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hdgA read from 3hdgA/T0634-3hdgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hdgA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3hdgA)A8 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 3hdgA 9 :LKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFGLHAPDVIITDIRMPKLGGLEMLDRIKAGG T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNY 3hdgA 79 :AKPYVIVISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFRHIKLA Number of specific fragments extracted= 2 number of extra gaps= 0 total=340 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h1gA/T0634-3h1gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3h1gA expands to /projects/compbio/data/pdb/3h1g.pdb.gz 3h1gA:# T0634 read from 3h1gA/T0634-3h1gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h1gA read from 3h1gA/T0634-3h1gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h1gA to template set # found chain 3h1gA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3h1gA)M1 T0634 5 :KILIIDQQDFSRIELKNFLD 3h1gA 2 :KLLVVDDSSTMRRIIKNTLS T0634 25 :SEY 3h1gA 23 :LGY T0634 28 :LVIESKNEKEALEQIDH 3h1gA 27 :DVLEAEHGVEAWEKLDA T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3h1gA 45 :ADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=344 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h1gA/T0634-3h1gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3h1gA/T0634-3h1gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h1gA read from 3h1gA/T0634-3h1gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h1gA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3h1gA)M1 T0634 5 :KILIIDQQ 3h1gA 2 :KLLVVDDS T0634 13 :DFSRI 3h1gA 11 :TMRRI T0634 19 :LKNFLDSE 3h1gA 16 :IKNTLSRL T0634 27 :YLVIESKNEKEALEQIDH 3h1gA 26 :EDVLEAEHGVEAWEKLDA T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3h1gA 45 :ADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMI T0634 84 :SSEHKEA 3h1gA 83 :TAEGGKA T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3h1gA 91 :VITALKAGVNNYIVKPFTPQVLKEKLEVVL Number of specific fragments extracted= 7 number of extra gaps= 0 total=351 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h1gA/T0634-3h1gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3h1gA/T0634-3h1gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h1gA read from 3h1gA/T0634-3h1gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h1gA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3h1gA)M1 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYL 3h1gA 2 :KLLVVDDSSTMRRIIKNTLSRLGYE T0634 29 :VIESKNEKEALEQIDH 3h1gA 28 :VLEAEHGVEAWEKLDA T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3h1gA 45 :ADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=354 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gwgA/T0634-3gwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gwgA expands to /projects/compbio/data/pdb/3gwg.pdb.gz 3gwgA:# T0634 read from 3gwgA/T0634-3gwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gwgA read from 3gwgA/T0634-3gwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gwgA to template set # found chain 3gwgA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3gwgA)M1 T0634 5 :KILIIDQQDFSRIELKNFLD 3gwgA 2 :KLLVVDDSSTMRRIIKNTLS T0634 25 :SEY 3gwgA 23 :LGY T0634 28 :LVIESKNEKEALEQIDH 3gwgA 27 :DVLEAEHGVEAWEKLDA T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3gwgA 45 :ADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=358 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gwgA/T0634-3gwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3gwgA/T0634-3gwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gwgA read from 3gwgA/T0634-3gwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gwgA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3gwgA)M1 T0634 5 :KILIIDQQ 3gwgA 2 :KLLVVDDS T0634 13 :DFSRI 3gwgA 11 :TMRRI T0634 19 :LKNFLDSE 3gwgA 16 :IKNTLSRL T0634 27 :YLVIESKNEKEALEQIDH 3gwgA 26 :EDVLEAEHGVEAWEKLDA T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3gwgA 45 :ADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMI T0634 84 :SSEHKEA 3gwgA 83 :TTEGGKA T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3gwgA 91 :VITALKAGVNNYIVKPFTPQVLKEKLEVVL Number of specific fragments extracted= 7 number of extra gaps= 0 total=365 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gwgA/T0634-3gwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3gwgA/T0634-3gwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gwgA read from 3gwgA/T0634-3gwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gwgA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3gwgA)M1 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYL 3gwgA 2 :KLLVVDDSSTMRRIIKNTLSRLGYE T0634 29 :VIESKNEKEALEQIDH 3gwgA 28 :VLEAEHGVEAWEKLDA T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3gwgA 45 :ADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=368 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qkkA/T0634-1qkkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qkkA expands to /projects/compbio/data/pdb/1qkk.pdb.gz 1qkkA:Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1qkkA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1qkkA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1qkkA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1qkkA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1qkkA Skipped atom 611, because occupancy 0.250 <= existing 0.500 in 1qkkA Skipped atom 612, because occupancy 0.250 <= existing 0.500 in 1qkkA Skipped atom 613, because occupancy 0.250 <= existing 0.500 in 1qkkA Skipped atom 614, because occupancy 0.250 <= existing 0.500 in 1qkkA Skipped atom 615, because occupancy 0.250 <= existing 0.500 in 1qkkA # T0634 read from 1qkkA/T0634-1qkkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qkkA read from 1qkkA/T0634-1qkkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qkkA to template set # found chain 1qkkA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (1qkkA)P5 T0634 5 :KILIIDQQDFSRIELKNFLD 1qkkA 6 :SVFLIDDDRDLRKAMQQTLE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1qkkA 27 :AGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILAL T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYS 1qkkA 74 :DPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLVM Number of specific fragments extracted= 3 number of extra gaps= 0 total=371 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qkkA/T0634-1qkkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1qkkA/T0634-1qkkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qkkA read from 1qkkA/T0634-1qkkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qkkA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (1qkkA)P5 T0634 5 :KILIIDQQD 1qkkA 6 :SVFLIDDDR T0634 14 :FSRI 1qkkA 16 :LRKA T0634 19 :LKNFLDSE 1qkkA 20 :MQQTLELA T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1qkkA 29 :FTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILAL T0634 74 :LKNVPLILL 1qkkA 74 :DPDLPMILV T0634 84 :SSEHKEA 1qkkA 83 :TGHGDIP T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 1qkkA 91 :AVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLV Number of specific fragments extracted= 7 number of extra gaps= 0 total=378 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qkkA/T0634-1qkkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1qkkA/T0634-1qkkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qkkA read from 1qkkA/T0634-1qkkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qkkA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1qkkA)P5 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1qkkA 6 :SVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILAL T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRKN 1qkkA 74 :DPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLVMENRSL Number of specific fragments extracted= 2 number of extra gaps= 0 total=380 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h1fA/T0634-3h1fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3h1fA expands to /projects/compbio/data/pdb/3h1f.pdb.gz 3h1fA:# T0634 read from 3h1fA/T0634-3h1fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h1fA read from 3h1fA/T0634-3h1fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h1fA to template set # found chain 3h1fA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3h1fA)M1 Warning: unaligning (T0634)F107 because of BadResidue code BAD_PEPTIDE in next template residue (3h1fA)T108 Warning: unaligning (T0634)N108 because of BadResidue code BAD_PEPTIDE at template residue (3h1fA)T108 T0634 5 :KILIIDQQDFSRIELKNFLD 3h1fA 2 :KLLVVDDSSTMRRIIKNTLS T0634 25 :SEY 3h1fA 23 :LGY T0634 28 :LVIESKNEKEALEQIDH 3h1fA 27 :DVLEAEHGVEAWEKLDA T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKP 3h1fA 45 :ADTKVLITAWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKP T0634 109 :RNDLLSRIEIHL 3h1fA 109 :PQVLKEKLEVVL Number of specific fragments extracted= 5 number of extra gaps= 1 total=385 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h1fA/T0634-3h1fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3h1fA/T0634-3h1fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h1fA read from 3h1fA/T0634-3h1fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h1fA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3h1fA)M1 Warning: unaligning (T0634)F107 because of BadResidue code BAD_PEPTIDE in next template residue (3h1fA)T108 Warning: unaligning (T0634)N108 because of BadResidue code BAD_PEPTIDE at template residue (3h1fA)T108 T0634 5 :KILIIDQQ 3h1fA 2 :KLLVVDDS T0634 13 :DFSRI 3h1fA 11 :TMRRI T0634 19 :LKNFLDSE 3h1fA 16 :IKNTLSRL T0634 27 :YLVIESKNEKEALEQIDH 3h1fA 26 :EDVLEAEHGVEAWEKLDA T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3h1fA 45 :ADTKVLITAWNMPEMNGLDLVKKVRSDSRFKEIPIIMI T0634 84 :SSEHKEA 3h1fA 83 :TTEGGKA T0634 91 :IVNGLHSGADDYLTKP 3h1fA 91 :VITALKAGVNNYIVKP T0634 109 :RNDLLSRIEIHL 3h1fA 109 :PQVLKEKLEVVL Number of specific fragments extracted= 8 number of extra gaps= 1 total=393 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h1fA/T0634-3h1fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3h1fA/T0634-3h1fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h1fA read from 3h1fA/T0634-3h1fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h1fA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3h1fA)M1 Warning: unaligning (T0634)F107 because of BadResidue code BAD_PEPTIDE in next template residue (3h1fA)T108 Warning: unaligning (T0634)N108 because of BadResidue code BAD_PEPTIDE at template residue (3h1fA)T108 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYL 3h1fA 2 :KLLVVDDSSTMRRIIKNTLSRLGYE T0634 29 :VIESKNEKEALEQIDH 3h1fA 28 :VLEAEHGVEAWEKLDA T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKP 3h1fA 45 :ADTKVLITAWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKP T0634 109 :RNDLLSRIEIHL 3h1fA 109 :PQVLKEKLEVVL Number of specific fragments extracted= 4 number of extra gaps= 1 total=397 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hdvA/T0634-3hdvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hdvA expands to /projects/compbio/data/pdb/3hdv.pdb.gz 3hdvA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 3hdvA/T0634-3hdvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hdvA read from 3hdvA/T0634-3hdvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hdvA to template set # found chain 3hdvA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3hdvA)R68 Warning: unaligning (T0634)S84 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hdvA)D151 Warning: unaligning (T0634)S85 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hdvA)D151 T0634 4 :KKILIIDQQDFSRIELKNFLD 3hdvA 69 :PLVLVVDDNAVNREALILYLK T0634 25 :SEYLVIESKNEKEALEQIDHHH 3hdvA 91 :RGIDAVGADGAEEARLYLHYQK T0634 47 :PDLVILDMDIIGENSPNLCLKLKRSK 3hdvA 114 :IGLMITDLRMQPESGLDLIRTIRASE T0634 74 :LKNVPLILLF 3hdvA 140 :RAALSIIVVS T0634 86 :EHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3hdvA 152 :TDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKEL Number of specific fragments extracted= 5 number of extra gaps= 1 total=402 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hdvA/T0634-3hdvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3hdvA/T0634-3hdvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hdvA read from 3hdvA/T0634-3hdvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hdvA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3hdvA)R68 Warning: unaligning (T0634)S85 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hdvA)D151 Warning: unaligning (T0634)E86 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hdvA)D151 Warning: unaligning (T0634)R121 because last residue in template chain is (3hdvA)K187 T0634 4 :KKILIIDQQ 3hdvA 69 :PLVLVVDDN T0634 13 :DFSRI 3hdvA 79 :VNREA T0634 19 :LKNFLDSE 3hdvA 84 :LILYLKSR T0634 27 :YLVIESKNEKEALEQIDH 3hdvA 93 :IDAVGADGAEEARLYLHY T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRS 3hdvA 112 :KRIGLMITDLRMQPESGLDLIRTIRAS T0634 73 :GLKNVPLILL 3hdvA 139 :ERAALSIIVV T0634 84 :S 3hdvA 149 :S T0634 87 :HKEA 3hdvA 152 :TDVE T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3hdvA 157 :AVDVMHLGVVDFLLKPVDLGKLLELVNKEL Number of specific fragments extracted= 9 number of extra gaps= 1 total=411 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hdvA/T0634-3hdvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3hdvA/T0634-3hdvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hdvA read from 3hdvA/T0634-3hdvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hdvA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3hdvA)R68 Warning: unaligning (T0634)S84 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hdvA)D151 Warning: unaligning (T0634)S85 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hdvA)D151 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDH 3hdvA 69 :PLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHY T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSK 3hdvA 112 :KRIGLMITDLRMQPESGLDLIRTIRASE T0634 74 :LKNVPLILLF 3hdvA 140 :RAALSIIVVS T0634 86 :EHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3hdvA 152 :TDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKEL Number of specific fragments extracted= 4 number of extra gaps= 1 total=415 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hebA/T0634-3hebA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hebA expands to /projects/compbio/data/pdb/3heb.pdb.gz 3hebA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 3hebA/T0634-3hebA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hebA read from 3hebA/T0634-3hebA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hebA to template set # found chain 3hebA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3hebA)V8 Warning: unaligning (T0634)K131 because last residue in template chain is (3hebA)G149 T0634 5 :KILIIDQQDFSRIELKNFLD 3hebA 9 :TIVMIEDDLGHARLIEKNIR T0634 25 :SEY 3hebA 30 :AGV T0634 28 :LVIESKNEKEALEQIDH 3hebA 35 :EIIAFTDGTSALNYLFG T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYS 3hebA 61 :GRAQLVLLDLNLPDMTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNYENFANAIRQLGLFFSVMQ T0634 128 :DLR 3hebA 146 :ETE Number of specific fragments extracted= 5 number of extra gaps= 0 total=420 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hebA/T0634-3hebA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3hebA/T0634-3hebA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hebA read from 3hebA/T0634-3hebA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hebA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3hebA)V8 Warning: unaligning (T0634)E133 because last residue in template chain is (3hebA)G149 T0634 5 :KILIIDQQ 3hebA 9 :TIVMIEDD T0634 13 :DFSRI 3hebA 18 :GHARL T0634 19 :LKNFLDSE 3hebA 23 :IEKNIRRA T0634 27 :YLVIESKNEKEALEQID 3hebA 34 :NEIIAFTDGTSALNYLF T0634 44 :HHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3hebA 60 :AGRAQLVLLDLNLPDMTGIDILKLVKENPHTRRSPVVIL T0634 84 :SSEHKEA 3hebA 99 :TTTDDQR T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRKN 3hebA 107 :IQRCYDLGANVYITKPVNYENFANAIRQLGLFFSVMQVPETE Number of specific fragments extracted= 7 number of extra gaps= 0 total=427 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hebA/T0634-3hebA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3hebA/T0634-3hebA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hebA read from 3hebA/T0634-3hebA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hebA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3hebA)V8 T0634 4 :KKILIIDQQDFSRIELKNFLDSEY 3hebA 9 :TIVMIEDDLGHARLIEKNIRRAGV T0634 28 :LVIESKNEKEALEQID 3hebA 35 :EIIAFTDGTSALNYLF T0634 44 :HHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 3hebA 60 :AGRAQLVLLDLNLPDMTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNYENFANAIRQLGLFF Number of specific fragments extracted= 3 number of extra gaps= 0 total=430 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dbwA/T0634-1dbwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dbwA expands to /projects/compbio/data/pdb/1dbw.pdb.gz 1dbwA:Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1dbwA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1dbwA # T0634 read from 1dbwA/T0634-1dbwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dbwA read from 1dbwA/T0634-1dbwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dbwA to template set # found chain 1dbwA in template set Warning: unaligning (T0634)N124 because last residue in template chain is (1dbwA)V123 T0634 1 :MSLKKILIIDQQDFSRIELKNFLD 1dbwA 1 :MQDYTVHIVDDEEPVRKSLAFMLT T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1dbwA 26 :NGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDL T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 1dbwA 73 :KINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHL Number of specific fragments extracted= 3 number of extra gaps= 0 total=433 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dbwA/T0634-1dbwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1dbwA/T0634-1dbwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dbwA read from 1dbwA/T0634-1dbwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dbwA in template set Warning: unaligning (T0634)N124 because last residue in template chain is (1dbwA)V123 T0634 1 :MSLKKILIIDQQD 1dbwA 1 :MQDYTVHIVDDEE T0634 14 :FSRI 1dbwA 15 :VRKS T0634 19 :LKNFLDSE 1dbwA 19 :LAFMLTMN T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1dbwA 28 :FAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLK T0634 75 :KNVPLILL 1dbwA 74 :INIPSIVI T0634 84 :SSEHKEA 1dbwA 82 :TGHGDVP T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 1dbwA 90 :AVEAMKAGAVDFIEKPFEDTVIIEAIERASEHL Number of specific fragments extracted= 7 number of extra gaps= 0 total=440 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dbwA/T0634-1dbwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1dbwA/T0634-1dbwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dbwA read from 1dbwA/T0634-1dbwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dbwA in template set T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1dbwA 2 :QDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLK T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRT 1dbwA 74 :INIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEH Number of specific fragments extracted= 2 number of extra gaps= 0 total=442 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rjnA/T0634-2rjnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2rjnA expands to /projects/compbio/data/pdb/2rjn.pdb.gz 2rjnA:# T0634 read from 2rjnA/T0634-2rjnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rjnA read from 2rjnA/T0634-2rjnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rjnA to template set # found chain 2rjnA in template set Warning: unaligning (T0634)S2 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rjnA)N7 Warning: unaligning (T0634)L3 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rjnA)N7 Warning: unaligning (T0634)L113 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rjnA)K118 Warning: unaligning (T0634)S114 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rjnA)K118 Warning: unaligning (T0634)G134 because last residue in template chain is (2rjnA)E138 T0634 1 :M 2rjnA 5 :Y T0634 4 :KKILIIDQQDFSRIELKNFLD 2rjnA 8 :YTVMLVDDEQPILNSLKRLIK T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2rjnA 30 :LGCNIITFTSPLDALEALKGTSVQLVISDMRMPEMGGEVFLEQVAKS T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSG 2rjnA 77 :YPDIERVVISGYADAQATIDAVNRG T0634 99 :ADDYLTKPFNRNDL 2rjnA 103 :ISRFLLKPWEDEDV T0634 115 :RIEIHLRTQNYYSD 2rjnA 119 :VVEKGLQLAFLREE T0634 131 :KNE 2rjnA 135 :RLQ Number of specific fragments extracted= 7 number of extra gaps= 2 total=449 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rjnA/T0634-2rjnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2rjnA/T0634-2rjnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rjnA read from 2rjnA/T0634-2rjnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rjnA in template set Warning: unaligning (T0634)S2 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rjnA)N7 Warning: unaligning (T0634)L3 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rjnA)N7 Warning: unaligning (T0634)L113 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rjnA)K118 Warning: unaligning (T0634)S114 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rjnA)K118 Warning: unaligning (T0634)G134 because last residue in template chain is (2rjnA)E138 T0634 1 :M 2rjnA 5 :Y T0634 4 :KKILIIDQQ 2rjnA 8 :YTVMLVDDE T0634 13 :DFSRI 2rjnA 18 :PILNS T0634 19 :LKNFLDSE 2rjnA 23 :LKRLIKRL T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2rjnA 32 :CNIITFTSPLDALEALKGTSVQLVISDMRMPEMGGEVFLEQVAKS T0634 74 :LKNVPLILL 2rjnA 77 :YPDIERVVI T0634 84 :SSEHK 2rjnA 86 :SGYAD T0634 94 :GLHSG 2rjnA 97 :AVNRG T0634 99 :ADDYLTKPFNRNDL 2rjnA 103 :ISRFLLKPWEDEDV T0634 115 :RIEIHLRTQNYYSDLRKNE 2rjnA 119 :VVEKGLQLAFLREENLRLQ Number of specific fragments extracted= 10 number of extra gaps= 2 total=459 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rjnA/T0634-2rjnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2rjnA/T0634-2rjnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rjnA read from 2rjnA/T0634-2rjnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rjnA in template set Warning: unaligning (T0634)S2 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rjnA)N7 Warning: unaligning (T0634)L113 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rjnA)K118 Warning: unaligning (T0634)S114 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rjnA)K118 Warning: unaligning (T0634)H137 because last residue in template chain is (2rjnA)E138 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2rjnA 8 :YTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALKGTSVQLVISDMRMPEMGGEVFLEQVAKS T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSG 2rjnA 77 :YPDIERVVISGYADAQATIDAVNRG T0634 99 :ADDYLTKPFNRNDL 2rjnA 103 :ISRFLLKPWEDEDV T0634 115 :RIEIHLRTQNYY 2rjnA 119 :VVEKGLQLAFLR T0634 130 :RKNEGHH 2rjnA 131 :EENLRLQ Number of specific fragments extracted= 5 number of extra gaps= 2 total=464 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ys7A/T0634-1ys7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ys7A expands to /projects/compbio/data/pdb/1ys7.pdb.gz 1ys7A:# T0634 read from 1ys7A/T0634-1ys7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys7A read from 1ys7A/T0634-1ys7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ys7A to template set # found chain 1ys7A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1ys7A)S7 Warning: unaligning (T0634)I51 because of BadResidue code BAD_PEPTIDE in next template residue (1ys7A)L57 Warning: unaligning (T0634)L52 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)L57 Warning: unaligning (T0634)H87 because of BadResidue code BAD_PEPTIDE in next template residue (1ys7A)V91 Warning: unaligning (T0634)K88 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)V91 Warning: unaligning (T0634)E89 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)D92 Warning: unaligning (T0634)V92 because of BadResidue code BAD_PEPTIDE in next template residue (1ys7A)A96 Warning: unaligning (T0634)N93 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)A96 T0634 4 :KKILIIDQQDFSRIELKNFLD 1ys7A 8 :PRVLVVDDDSDVLASLERGLR T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLV 1ys7A 30 :SGFEVATAVDGAEALRSATENRPDAI T0634 53 :DMDIIGENSPNLCLKLKRS 1ys7A 58 :DINMPVLDGVSVVTALRAM T0634 74 :LKNVPLILLFSSE 1ys7A 77 :DNDVPVCVLSARS T0634 90 :AI 1ys7A 93 :DR T0634 94 :GLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRKNEGHHH 1ys7A 97 :GLEAGADDYLVKPFVLAELVARVKALLRRRGSTATSSSETITVG Number of specific fragments extracted= 6 number of extra gaps= 3 total=470 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ys7A/T0634-1ys7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1ys7A/T0634-1ys7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys7A read from 1ys7A/T0634-1ys7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ys7A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1ys7A)S7 Warning: unaligning (T0634)I51 because of BadResidue code BAD_PEPTIDE in next template residue (1ys7A)L57 Warning: unaligning (T0634)L52 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)L57 Warning: unaligning (T0634)K88 because of BadResidue code BAD_PEPTIDE in next template residue (1ys7A)V91 Warning: unaligning (T0634)E89 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)V91 Warning: unaligning (T0634)A90 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)D92 Warning: unaligning (T0634)V92 because of BadResidue code BAD_PEPTIDE in next template residue (1ys7A)A96 Warning: unaligning (T0634)N93 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)A96 T0634 4 :KKILIIDQQ 1ys7A 8 :PRVLVVDDD T0634 13 :DFSRI 1ys7A 18 :DVLAS T0634 19 :LKNFLDSE 1ys7A 23 :LERGLRLS T0634 27 :YLVIESKNEKEALEQIDHHHPDLV 1ys7A 32 :FEVATAVDGAEALRSATENRPDAI T0634 53 :DMDIIGENSPNLCLKLKRSK 1ys7A 58 :DINMPVLDGVSVVTALRAMD T0634 75 :KNVPLILL 1ys7A 78 :NDVPVCVL T0634 84 :SSEH 1ys7A 86 :SARS T0634 91 :I 1ys7A 94 :R T0634 94 :GLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRKNEGHH 1ys7A 97 :GLEAGADDYLVKPFVLAELVARVKALLRRRGSTATSSSETITV Number of specific fragments extracted= 9 number of extra gaps= 3 total=479 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ys7A/T0634-1ys7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1ys7A/T0634-1ys7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys7A read from 1ys7A/T0634-1ys7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ys7A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1ys7A)S7 Warning: unaligning (T0634)I51 because of BadResidue code BAD_PEPTIDE in next template residue (1ys7A)L57 Warning: unaligning (T0634)L52 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)L57 Warning: unaligning (T0634)H87 because of BadResidue code BAD_PEPTIDE in next template residue (1ys7A)V91 Warning: unaligning (T0634)K88 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)V91 Warning: unaligning (T0634)E89 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)D92 Warning: unaligning (T0634)V92 because of BadResidue code BAD_PEPTIDE in next template residue (1ys7A)A96 Warning: unaligning (T0634)N93 because of BadResidue code BAD_PEPTIDE at template residue (1ys7A)A96 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLV 1ys7A 8 :PRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSATENRPDAI T0634 53 :DMDIIGENSPNLCLKLKRSK 1ys7A 58 :DINMPVLDGVSVVTALRAMD T0634 75 :KNVPLILLFSSE 1ys7A 78 :NDVPVCVLSARS T0634 90 :AI 1ys7A 93 :DR T0634 94 :GLHSGADDYLTKPFNRNDLLSRIEIHLRTQNY 1ys7A 97 :GLEAGADDYLVKPFVLAELVARVKALLRRRGS Number of specific fragments extracted= 5 number of extra gaps= 3 total=484 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h5iA/T0634-3h5iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3h5iA expands to /projects/compbio/data/pdb/3h5i.pdb.gz 3h5iA:Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 515, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 519, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 3h5iA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 3h5iA # T0634 read from 3h5iA/T0634-3h5iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h5iA read from 3h5iA/T0634-3h5iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h5iA to template set # found chain 3h5iA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3h5iA)K4 T0634 5 :KILIIDQQDFSRIELKNFLD 3h5iA 5 :KILIVEDSKFQAKTIANILN T0634 25 :SEYLVIESKNEKEALEQIDHHH 3h5iA 26 :YGYTVEIALTGEAAVEKVSGGW T0634 47 :PDLVILDMDIIG 3h5iA 49 :PDLILMDIELGE T0634 59 :ENSPNLCLKLKRS 3h5iA 62 :MDGVQTALAIQQI T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYS 3h5iA 75 :SELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMALRLYEANV Number of specific fragments extracted= 5 number of extra gaps= 0 total=489 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h5iA/T0634-3h5iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3h5iA/T0634-3h5iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h5iA read from 3h5iA/T0634-3h5iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h5iA in template set Warning: unaligning (T0634)K4 because first residue in template chain is (3h5iA)K4 Warning: unaligning (T0634)D128 because last residue in template chain is (3h5iA)H128 T0634 5 :KILIIDQQ 3h5iA 5 :KILIVEDS T0634 13 :DFSRI 3h5iA 14 :FQAKT T0634 19 :LKNFLDSE 3h5iA 19 :IANILNKY T0634 27 :YLVIESKNEKEALEQIDHH 3h5iA 28 :YTVEIALTGEAAVEKVSGG T0634 46 :HPDLVILDMDIIG 3h5iA 48 :YPDLILMDIELGE T0634 59 :ENSPNLCLKLKRS 3h5iA 62 :MDGVQTALAIQQI T0634 75 :KNVPLILL 3h5iA 75 :SELPVVFL T0634 84 :SSEHKEA 3h5iA 83 :TAHTEPA T0634 93 :NGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYS 3h5iA 93 :KIRSVTAYGYVMKSATEQVLITIVEMALRLYEANV Number of specific fragments extracted= 9 number of extra gaps= 0 total=498 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h5iA/T0634-3h5iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3h5iA/T0634-3h5iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h5iA read from 3h5iA/T0634-3h5iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h5iA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3h5iA)K4 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHH 3h5iA 5 :KILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVSGG T0634 46 :HPDLVILDMDIIGENSPNLCLKLKRS 3h5iA 48 :YPDLILMDIELGEGMDGVQTALAIQQ T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 3h5iA 74 :ISELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMALRLYEAN Number of specific fragments extracted= 3 number of extra gaps= 0 total=501 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gkgA/T0634-2gkgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2gkgA/T0634-2gkgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gkgA read from 2gkgA/T0634-2gkgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gkgA in training set Warning: unaligning (T0634)K4 because first residue in template chain is (2gkgA)K3 T0634 5 :KILIIDQQDFSRIELKNFLD 2gkgA 4 :KILIVESDTALSATLRSALE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDII 2gkgA 25 :RGFTVDETTDGKGSVEQIRRDRPDLVVLAVDLS T0634 58 :GENSPNLCLKLKRSKGLKNVPLILL 2gkgA 59 :GQNGYLICGKLKKDDDLKNVPIVII T0634 84 :SSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 2gkgA 84 :GNPDGFAQHRKLKAHADEYVAKPVDADQLVERAGALI Number of specific fragments extracted= 4 number of extra gaps= 0 total=505 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gkgA/T0634-2gkgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2gkgA/T0634-2gkgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gkgA read from 2gkgA/T0634-2gkgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gkgA in training set Warning: unaligning (T0634)K4 because first residue in template chain is (2gkgA)K3 T0634 5 :KILIIDQQ 2gkgA 4 :KILIVESD T0634 13 :DFSRI 2gkgA 13 :ALSAT T0634 19 :LKNFLDSE 2gkgA 18 :LRSALEGR T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDII 2gkgA 27 :FTVDETTDGKGSVEQIRRDRPDLVVLAVDLS T0634 58 :GENSPNLCLKLKRSKGLKNVPLILL 2gkgA 59 :GQNGYLICGKLKKDDDLKNVPIVII T0634 84 :SSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 2gkgA 84 :GNPDGFAQHRKLKAHADEYVAKPVDADQLVERAGALI Number of specific fragments extracted= 6 number of extra gaps= 0 total=511 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gkgA/T0634-2gkgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2gkgA/T0634-2gkgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gkgA read from 2gkgA/T0634-2gkgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gkgA in training set Warning: unaligning (T0634)L3 because first residue in template chain is (2gkgA)K3 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIG 2gkgA 4 :KILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIRRDRPDLVVLAVDLSA T0634 59 :ENSPNLCLKLKRSKGLKNVPLIL 2gkgA 60 :QNGYLICGKLKKDDDLKNVPIVI T0634 83 :FSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 2gkgA 83 :IGNPDGFAQHRKLKAHADEYVAKPVDADQLVERAGALI Number of specific fragments extracted= 3 number of extra gaps= 0 total=514 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pl1A/T0634-2pl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pl1A expands to /projects/compbio/data/pdb/2pl1.pdb.gz 2pl1A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 2pl1A/T0634-2pl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pl1A read from 2pl1A/T0634-2pl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pl1A to template set # found chain 2pl1A in template set Warning: unaligning (T0634)K4 because first residue in template chain is (2pl1A)M1 T0634 5 :KILIIDQQDFSRIELKNFLD 2pl1A 2 :RVLVVEDNALLRHHLKVQIQ T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2pl1A 23 :AGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSN T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 2pl1A 70 :DVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRRNS Number of specific fragments extracted= 3 number of extra gaps= 0 total=517 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pl1A/T0634-2pl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2pl1A/T0634-2pl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pl1A read from 2pl1A/T0634-2pl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pl1A in template set Warning: unaligning (T0634)K4 because first residue in template chain is (2pl1A)M1 T0634 5 :KILIIDQQ 2pl1A 2 :RVLVVEDN T0634 13 :DFSRI 2pl1A 11 :LLRHH T0634 19 :LKNFLDSE 2pl1A 16 :LKVQIQDA T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 2pl1A 25 :HQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSND T0634 75 :KNVPLILL 2pl1A 71 :VSLPILVL T0634 84 :SSEHKEA 2pl1A 79 :TARESWQ T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 2pl1A 87 :KVEVLSAGADDYVTKPFHIEEVMARMQALMRRNS Number of specific fragments extracted= 7 number of extra gaps= 0 total=524 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pl1A/T0634-2pl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2pl1A/T0634-2pl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pl1A read from 2pl1A/T0634-2pl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pl1A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2pl1A)M1 T0634 4 :KKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 2pl1A 2 :RVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSND T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 2pl1A 71 :VSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRRNS Number of specific fragments extracted= 2 number of extra gaps= 0 total=526 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mvoA/T0634-1mvoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mvoA expands to /projects/compbio/data/pdb/1mvo.pdb.gz 1mvoA:Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1mvoA # T0634 read from 1mvoA/T0634-1mvoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mvoA read from 1mvoA/T0634-1mvoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mvoA to template set # found chain 1mvoA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1mvoA)M1 Warning: unaligning (T0634)Q123 because last residue in template chain is (1mvoA)S121 T0634 3 :LKKILIIDQQDFSRIELKNFLD 1mvoA 2 :NKKILVVDDEESIVTLLQYNLE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1mvoA 25 :SGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQ T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRT 1mvoA 72 :KLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRR Number of specific fragments extracted= 3 number of extra gaps= 0 total=529 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mvoA/T0634-1mvoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1mvoA/T0634-1mvoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mvoA read from 1mvoA/T0634-1mvoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mvoA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1mvoA)M1 Warning: unaligning (T0634)Q123 because last residue in template chain is (1mvoA)S121 T0634 3 :LKKILIIDQQD 1mvoA 2 :NKKILVVDDEE T0634 14 :FSRI 1mvoA 14 :IVTL T0634 19 :LKNFLDSE 1mvoA 18 :LQYNLERS T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1mvoA 27 :YDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQK T0634 75 :KNVPLILL 1mvoA 73 :LMFPILML T0634 84 :SSEHKEA 1mvoA 81 :TAKDEEF T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRT 1mvoA 89 :KVLGLELGADDYMTKPFSPREVNARVKAILRR Number of specific fragments extracted= 7 number of extra gaps= 0 total=536 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mvoA/T0634-1mvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1mvoA/T0634-1mvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mvoA read from 1mvoA/T0634-1mvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mvoA in template set Warning: unaligning (T0634)Q123 because last residue in template chain is (1mvoA)S121 T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1mvoA 1 :MNKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQK T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRT 1mvoA 73 :LMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRR Number of specific fragments extracted= 2 number of extra gaps= 0 total=538 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hv2A/T0634-3hv2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hv2A expands to /projects/compbio/data/pdb/3hv2.pdb.gz 3hv2A:Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 206, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 208, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 210, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 212, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 242, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 244, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 815, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1049, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1057, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 3hv2A Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 3hv2A # T0634 read from 3hv2A/T0634-3hv2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hv2A read from 3hv2A/T0634-3hv2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hv2A to template set # found chain 3hv2A in template set Warning: unaligning (T0634)R130 because last residue in template chain is (3hv2A)L139 T0634 1 :MSLKKILIIDQQDFSRIELKNFLD 3hv2A 10 :TRRPEILLVDSQEVILQRLQQLLS T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 3hv2A 35 :LPYTLHFARDATQALQLLASREVDLVISAAHLPQMDGPTLLARIHQQ T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSG 3hv2A 82 :YPSTTRILLTGDPDLKLIAKAINEG T0634 99 :ADDYLTKPFNRNDLLSRIEIHLRTQNYYSDL 3hv2A 108 :IYRYLSKPWDDQELLLALRQALEHQHSERER Number of specific fragments extracted= 4 number of extra gaps= 0 total=542 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hv2A/T0634-3hv2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3hv2A/T0634-3hv2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hv2A read from 3hv2A/T0634-3hv2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hv2A in template set T0634 2 :SLKKILIIDQQ 3hv2A 11 :RRPEILLVDSQ T0634 13 :DFSRI 3hv2A 23 :VILQR T0634 19 :LKNFLDSE 3hv2A 28 :LQQLLSPL T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 3hv2A 37 :YTLHFARDATQALQLLASREVDLVISAAHLPQMDGPTLLARIHQQ T0634 74 :LKNVPLILL 3hv2A 82 :YPSTTRILL T0634 84 :SSEHK 3hv2A 91 :TGDPD T0634 96 :HSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSD 3hv2A 105 :EGEIYRYLSKPWDDQELLLALRQALEHQHSERE Number of specific fragments extracted= 7 number of extra gaps= 0 total=549 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hv2A/T0634-3hv2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3hv2A/T0634-3hv2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hv2A read from 3hv2A/T0634-3hv2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hv2A in template set T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 3hv2A 11 :RRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLASREVDLVISAAHLPQMDGPTLLARIHQQ T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSG 3hv2A 82 :YPSTTRILLTGDPDLKLIAKAINEG T0634 99 :ADDYLTKPFNRNDLLSRIEIHLRTQNYYSD 3hv2A 108 :IYRYLSKPWDDQELLLALRQALEHQHSERE Number of specific fragments extracted= 3 number of extra gaps= 0 total=552 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3luaA/T0634-3luaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3luaA expands to /projects/compbio/data/pdb/3lua.pdb.gz 3luaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 3luaA/T0634-3luaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3luaA read from 3luaA/T0634-3luaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3luaA to template set # found chain 3luaA in template set T0634 3 :LKKILIIDQQDFSRIELKNFLD 3luaA 2 :DGTVLLIDYFEYEREKTKIIFD T0634 25 :SEYLVIESKNEKEALEQIDH 3luaA 26 :GEYDFIEVENLKKFYSIFKD T0634 45 :HHPDLVILDMDIIG 3luaA 47 :DSITLIIMDIAFPV T0634 59 :ENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3luaA 62 :KEGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVRSVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=556 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3luaA/T0634-3luaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3luaA/T0634-3luaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3luaA read from 3luaA/T0634-3luaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3luaA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3luaA)L-1 Warning: unaligning (T0634)T122 because last residue in template chain is (3luaA)I125 T0634 3 :LKKILIIDQQ 3luaA 2 :DGTVLLIDYF T0634 13 :DFSRI 3luaA 13 :YEREK T0634 19 :LKNFLDSE 3luaA 18 :TKIIFDNI T0634 27 :YLVIESKNEKEALEQIDH 3luaA 28 :YDFIEVENLKKFYSIFKD T0634 45 :HHPDLVILDMDIIG 3luaA 47 :DSITLIIMDIAFPV T0634 59 :ENSPNLCLKLKRSKGLKNVPLILL 3luaA 62 :KEGLEVLSAIRNNSRTANTPVIIA T0634 84 :SSEHKEA 3luaA 86 :TKSDNPG T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 3luaA 94 :RHAALKFKVSDYILKPYPTKRLENSVRSVLK Number of specific fragments extracted= 8 number of extra gaps= 0 total=564 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3luaA/T0634-3luaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3luaA/T0634-3luaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3luaA read from 3luaA/T0634-3luaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3luaA in template set T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSE 3luaA -1 :LDGTVLLIDYFEYEREKTKIIFDNIG T0634 27 :YLVIESKNEKEALEQIDH 3luaA 28 :YDFIEVENLKKFYSIFKD T0634 45 :HHPDLVILDMDIIG 3luaA 47 :DSITLIIMDIAFPV T0634 59 :ENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3luaA 62 :KEGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVRSVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=568 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1srrA/T0634-1srrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1srrA expands to /projects/compbio/data/pdb/1srr.pdb.gz 1srrA:# T0634 read from 1srrA/T0634-1srrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1srrA read from 1srrA/T0634-1srrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1srrA to template set # found chain 1srrA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1srrA)N3 Warning: unaligning (T0634)S85 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1srrA)G85 Warning: unaligning (T0634)E86 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1srrA)G85 T0634 4 :KKILIIDQQDFSRIELKNFLD 1srrA 4 :EKILIVDDQSGIRILLNEVFN T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1srrA 26 :EGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVI T0634 74 :LKNVPLILLFS 1srrA 73 :DENIRVIIMTA T0634 87 :HKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 1srrA 86 :ELDMIQESKELGALTHFAKPFDIDEIRDAVKKYLP Number of specific fragments extracted= 4 number of extra gaps= 1 total=572 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1srrA/T0634-1srrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1srrA/T0634-1srrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1srrA read from 1srrA/T0634-1srrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1srrA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1srrA)N3 Warning: unaligning (T0634)E86 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1srrA)G85 Warning: unaligning (T0634)H87 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1srrA)G85 Warning: unaligning (T0634)T122 because last residue in template chain is (1srrA)L121 T0634 4 :KKILIIDQQD 1srrA 4 :EKILIVDDQS T0634 14 :FSRI 1srrA 15 :IRIL T0634 19 :LKNFLDSE 1srrA 19 :LNEVFNKE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1srrA 28 :YQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVI T0634 74 :LKNVPLILL 1srrA 73 :DENIRVIIM T0634 84 :SS 1srrA 82 :TA T0634 88 :KEA 1srrA 86 :ELD T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 1srrA 90 :IQESKELGALTHFAKPFDIDEIRDAVKKYLP Number of specific fragments extracted= 8 number of extra gaps= 1 total=580 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1srrA/T0634-1srrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1srrA/T0634-1srrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1srrA read from 1srrA/T0634-1srrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1srrA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1srrA)N3 Warning: unaligning (T0634)S85 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1srrA)G85 Warning: unaligning (T0634)E86 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1srrA)G85 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1srrA 4 :EKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVI T0634 74 :LKNVPLILLFS 1srrA 73 :DENIRVIIMTA T0634 87 :HKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIH 1srrA 86 :ELDMIQESKELGALTHFAKPFDIDEIRDAVKKY Number of specific fragments extracted= 3 number of extra gaps= 1 total=583 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kcnA/T0634-3kcnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3kcnA expands to /projects/compbio/data/pdb/3kcn.pdb.gz 3kcnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0634 read from 3kcnA/T0634-3kcnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kcnA read from 3kcnA/T0634-3kcnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3kcnA to template set # found chain 3kcnA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3kcnA)L5 Warning: unaligning (T0634)S84 because of BadResidue code BAD_PEPTIDE in next template residue (3kcnA)N87 Warning: unaligning (T0634)S85 because of BadResidue code BAD_PEPTIDE at template residue (3kcnA)N87 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHH 3kcnA 6 :NERILLVDDDYSLLNTLKRNLSFDFEVTTCESGPEALACIKKSD T0634 47 :PDLVILDMDIIGENSPNLCLKLKRS 3kcnA 51 :FSVIMVDMRMPGMEGTEVIQKARLI T0634 74 :LKNVPLILLF 3kcnA 76 :SPNSVYLMLT T0634 86 :EHKEAIVNGLHSG 3kcnA 88 :QDLTTAMEAVNEG T0634 99 :ADDYLTKPFNRNDLLSRIEIHLRTQNYYSD 3kcnA 102 :VFRFLNKPCQMSDIKAAINAGIKQYDLVTS Number of specific fragments extracted= 5 number of extra gaps= 1 total=588 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kcnA/T0634-3kcnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3kcnA/T0634-3kcnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kcnA read from 3kcnA/T0634-3kcnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kcnA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3kcnA)L5 Warning: unaligning (T0634)S85 because of BadResidue code BAD_PEPTIDE in next template residue (3kcnA)N87 Warning: unaligning (T0634)E86 because of BadResidue code BAD_PEPTIDE at template residue (3kcnA)N87 T0634 3 :LKKILIIDQQ 3kcnA 6 :NERILLVDDD T0634 13 :DFSRI 3kcnA 17 :SLLNT T0634 19 :LKNFLDSEYLVIESKNEKEALEQIDHHHP 3kcnA 22 :LKRNLSFDFEVTTCESGPEALACIKKSDP T0634 48 :DLVILDMDIIGENSPNLCLKLKRS 3kcnA 52 :SVIMVDMRMPGMEGTEVIQKARLI T0634 74 :LKNVPLILL 3kcnA 76 :SPNSVYLML T0634 84 :S 3kcnA 85 :T T0634 87 :HK 3kcnA 88 :QD T0634 97 :SGADDYLTKPFNRNDLLSRIEIHLRTQ 3kcnA 100 :GQVFRFLNKPCQMSDIKAAINAGIKQY Number of specific fragments extracted= 8 number of extra gaps= 1 total=596 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kcnA/T0634-3kcnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3kcnA/T0634-3kcnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kcnA read from 3kcnA/T0634-3kcnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kcnA in template set Warning: unaligning (T0634)S84 because of BadResidue code BAD_PEPTIDE in next template residue (3kcnA)N87 Warning: unaligning (T0634)S85 because of BadResidue code BAD_PEPTIDE at template residue (3kcnA)N87 T0634 1 :MSLKKILIIDQQDFSRIELKNFLDS 3kcnA 5 :LNERILLVDDDYSLLNTLKRNLSFD T0634 27 :YLVIESKNEKEALEQIDHH 3kcnA 30 :FEVTTCESGPEALACIKKS T0634 46 :HPDLVILDMDIIGENSPNLCLKLKRS 3kcnA 50 :PFSVIMVDMRMPGMEGTEVIQKARLI T0634 74 :LKNVPLILLF 3kcnA 76 :SPNSVYLMLT T0634 86 :EHKEAIVNGLHSG 3kcnA 88 :QDLTTAMEAVNEG T0634 99 :ADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRKNE 3kcnA 102 :VFRFLNKPCQMSDIKAAINAGIKQYDLVTSKEELL Number of specific fragments extracted= 6 number of extra gaps= 1 total=602 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3jteA/T0634-3jteA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3jteA expands to /projects/compbio/data/pdb/3jte.pdb.gz 3jteA:# T0634 read from 3jteA/T0634-3jteA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jteA read from 3jteA/T0634-3jteA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3jteA to template set # found chain 3jteA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3jteA)L3 Warning: unaligning (T0634)S127 because last residue in template chain is (3jteA)M128 T0634 4 :KKILIIDQQDFSRIELKNFLD 3jteA 4 :AKILVIDDESTILQNIKFLLE T0634 25 :SEYLVIESKNEKEALEQIDH 3jteA 26 :DGNEVLTASSSTEGLRIFTE T0634 45 :HHPDLVILDMDIIGENSPNLCLKLKRS 3jteA 48 :NSIDVVITDMKMPKLSGMDILREIKKI T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 3jteA 75 :TPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAINRKKLL Number of specific fragments extracted= 4 number of extra gaps= 0 total=606 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3jteA/T0634-3jteA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3jteA/T0634-3jteA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jteA read from 3jteA/T0634-3jteA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3jteA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3jteA)L3 Warning: unaligning (T0634)S127 because last residue in template chain is (3jteA)M128 T0634 4 :KKILIIDQQ 3jteA 4 :AKILVIDDE T0634 13 :DFSRI 3jteA 14 :TILQN T0634 19 :LKNFLDSE 3jteA 19 :IKFLLEID T0634 27 :YLVIESKNEKEALEQIDHH 3jteA 28 :NEVLTASSSTEGLRIFTEN T0634 46 :HPDLVILDMDIIGENSPNLCLKLKRS 3jteA 49 :SIDVVITDMKMPKLSGMDILREIKKI T0634 74 :LKNVPLILL 3jteA 75 :TPHMAVIIL T0634 84 :SSEH 3jteA 84 :TGHG T0634 93 :NGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 3jteA 94 :LAMKEGAFEYLRKPVTAQDLSIAINNAINRKKLL Number of specific fragments extracted= 8 number of extra gaps= 0 total=614 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3jteA/T0634-3jteA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3jteA/T0634-3jteA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jteA read from 3jteA/T0634-3jteA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3jteA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3jteA)L3 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHH 3jteA 4 :AKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTEN T0634 46 :HPDLVILDMDIIGENSPNLCLKLKRS 3jteA 49 :SIDVVITDMKMPKLSGMDILREIKKI T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 3jteA 75 :TPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAINRKKLL Number of specific fragments extracted= 3 number of extra gaps= 0 total=617 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qr3A/T0634-2qr3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qr3A expands to /projects/compbio/data/pdb/2qr3.pdb.gz 2qr3A:Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 2qr3A Skipped atom 347, because occupancy 0.500 <= existing 0.500 in 2qr3A Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 2qr3A Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 2qr3A Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 2qr3A Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 2qr3A Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 2qr3A Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 2qr3A Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 2qr3A Skipped atom 931, because occupancy 0.500 <= existing 0.500 in 2qr3A # T0634 read from 2qr3A/T0634-2qr3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qr3A read from 2qr3A/T0634-2qr3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qr3A to template set # found chain 2qr3A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (2qr3A)S0 Warning: unaligning (T0634)E59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qr3A)N63 T0634 3 :LKKILIIDQQDFSRIELKNFLD 2qr3A 1 :LGTIIIVDDNKGVLTAVQLLLK T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDII 2qr3A 24 :HFSKVITLSSPVSLSTVLREENPEVVLLDMNFT T0634 60 :NSPNLCLKLKRS 2qr3A 64 :EGLFWLHEIKRQ T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 2qr3A 76 :YRDLPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLNAAS Number of specific fragments extracted= 4 number of extra gaps= 0 total=621 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qr3A/T0634-2qr3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2qr3A/T0634-2qr3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qr3A read from 2qr3A/T0634-2qr3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qr3A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (2qr3A)S0 Warning: unaligning (T0634)E59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qr3A)N63 T0634 3 :LKKILIIDQQ 2qr3A 1 :LGTIIIVDDN T0634 13 :DFSRI 2qr3A 12 :GVLTA T0634 19 :LKNFLDSE 2qr3A 17 :VQLLLKNH T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDII 2qr3A 26 :SKVITLSSPVSLSTVLREENPEVVLLDMNFT T0634 60 :NSPNLCLKLKRS 2qr3A 64 :EGLFWLHEIKRQ T0634 74 :LKNVPLILL 2qr3A 76 :YRDLPVVLF T0634 84 :SSEHKEA 2qr3A 85 :TAYADID T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHL 2qr3A 93 :AVRGIKEGASDFVVKPWDNQKLLETLLNAA Number of specific fragments extracted= 8 number of extra gaps= 0 total=629 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qr3A/T0634-2qr3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 2qr3A/T0634-2qr3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qr3A read from 2qr3A/T0634-2qr3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qr3A in template set Warning: unaligning (T0634)G58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qr3A)N63 Warning: unaligning (T0634)E59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qr3A)N63 T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDII 2qr3A 0 :SLGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLREENPEVVLLDMNFT T0634 60 :NSPNLCLKLKRS 2qr3A 64 :EGLFWLHEIKRQ T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 2qr3A 76 :YRDLPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLNAAS Number of specific fragments extracted= 3 number of extra gaps= 0 total=632 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i5aA/T0634-3i5aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3i5aA expands to /projects/compbio/data/pdb/3i5a.pdb.gz 3i5aA:# T0634 read from 3i5aA/T0634-3i5aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i5aA read from 3i5aA/T0634-3i5aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3i5aA to template set # found chain 3i5aA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3i5aA)S16 Warning: unaligning (T0634)S84 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i5aA)K100 Warning: unaligning (T0634)S85 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i5aA)K100 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i5aA)L121 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i5aA)L121 T0634 4 :KKILIIDQQDFSRIELKNFLD 3i5aA 17 :AMVLLVDDQAMIGEAVRRGLA T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLF 3i5aA 40 :ESIDFHFCADPHQAIAQAVQIKPTVILQDLVMPGLDGLTLVREYRSNPLTRDIPIIVLS T0634 86 :EHKEAIVNGLHSGADDYLT 3i5aA 101 :EDPLIKSAAFAAGANDYLV T0634 107 :FNRNDLLSRIEIHLRTQNYY 3i5aA 122 :PDNIELVARIRYHSRSYMTL Number of specific fragments extracted= 4 number of extra gaps= 2 total=636 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i5aA/T0634-3i5aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3i5aA/T0634-3i5aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i5aA read from 3i5aA/T0634-3i5aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i5aA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3i5aA)S16 Warning: unaligning (T0634)S85 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i5aA)K100 Warning: unaligning (T0634)E86 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i5aA)K100 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i5aA)L121 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i5aA)L121 T0634 4 :KKILIIDQQ 3i5aA 17 :AMVLLVDDQ T0634 13 :DFSRI 3i5aA 27 :MIGEA T0634 19 :LKNFLDSE 3i5aA 32 :VRRGLAGH T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3i5aA 42 :IDFHFCADPHQAIAQAVQIKPTVILQDLVMPGLDGLTLVREYRSNPLTRDIPIIVL T0634 84 :S 3i5aA 98 :S T0634 87 :HKEA 3i5aA 101 :EDPL T0634 91 :IVNGLHSGADDYLT 3i5aA 106 :KSAAFAAGANDYLV T0634 107 :FNRNDLLSRIEIHLRT 3i5aA 122 :PDNIELVARIRYHSRS Number of specific fragments extracted= 8 number of extra gaps= 2 total=644 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i5aA/T0634-3i5aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3i5aA/T0634-3i5aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i5aA read from 3i5aA/T0634-3i5aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i5aA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3i5aA)S16 Warning: unaligning (T0634)S84 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i5aA)K100 Warning: unaligning (T0634)S85 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i5aA)K100 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i5aA)L121 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i5aA)L121 T0634 3 :LKKILIIDQQDFSRIELKNFLDSE 3i5aA 17 :AMVLLVDDQAMIGEAVRRGLAGHE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLF 3i5aA 42 :IDFHFCADPHQAIAQAVQIKPTVILQDLVMPGLDGLTLVREYRSNPLTRDIPIIVLS T0634 86 :EHKEAIVNGLHSGADDYLT 3i5aA 101 :EDPLIKSAAFAAGANDYLV T0634 107 :FNRNDLLSRIEIHLRTQNYYSDLRK 3i5aA 122 :PDNIELVARIRYHSRSYMTLLQRDE Number of specific fragments extracted= 4 number of extra gaps= 2 total=648 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3breA/T0634-3breA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3breA expands to /projects/compbio/data/pdb/3bre.pdb.gz 3breA:# T0634 read from 3breA/T0634-3breA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3breA read from 3breA/T0634-3breA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3breA to template set # found chain 3breA in template set T0634 4 :KKILIIDQQDFSRIELKNFLD 3breA 19 :VMVLLVDDQAMIGEAVRRSLA T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 3breA 42 :AGIDFHFCSDPQQAVAVANQIKPTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRYHSRSYIAL Number of specific fragments extracted= 2 number of extra gaps= 0 total=650 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3breA/T0634-3breA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3breA/T0634-3breA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3breA read from 3breA/T0634-3breA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3breA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (3breA)A18 T0634 4 :KKILIIDQQDFSRIELKNFLDSE 3breA 19 :VMVLLVDDQAMIGEAVRRSLASE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 3breA 44 :IDFHFCSDPQQAVAVANQIKPTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVL T0634 84 :SSEHKEA 3breA 100 :STKEEPT T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRT 3breA 108 :KSAAFAAGANDYLVKLPDAIELVARIRYHSRS Number of specific fragments extracted= 4 number of extra gaps= 0 total=654 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3breA/T0634-3breA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 3breA/T0634-3breA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3breA read from 3breA/T0634-3breA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3breA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3breA)A18 T0634 3 :LKKILIIDQQDFSRIELKNFLDSE 3breA 19 :VMVLLVDDQAMIGEAVRRSLASEA T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRKN 3breA 44 :IDFHFCSDPQQAVAVANQIKPTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRYHSRSYIALQQRDEA Number of specific fragments extracted= 2 number of extra gaps= 0 total=656 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w25A/T0634-1w25A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w25A expands to /projects/compbio/data/pdb/1w25.pdb.gz 1w25A:# T0634 read from 1w25A/T0634-1w25A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w25A read from 1w25A/T0634-1w25A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w25A to template set # found chain 1w25A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1w25A)S2 T0634 4 :KKILIIDQQDFSRIELKNFLD 1w25A 3 :ARILVVDDIEANVRLLEAKLT T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSD 1w25A 25 :EYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFKLVIDE Number of specific fragments extracted= 2 number of extra gaps= 0 total=658 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w25A/T0634-1w25A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1w25A/T0634-1w25A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w25A read from 1w25A/T0634-1w25A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w25A in template set Warning: unaligning (T0634)L3 because first residue in template chain is (1w25A)S2 T0634 4 :KKILIIDQQ 1w25A 3 :ARILVVDDI T0634 13 :DFSRI 1w25A 13 :ANVRL T0634 19 :LKNFLDSE 1w25A 18 :LEAKLTAE T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILL 1w25A 27 :YEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLI T0634 84 :SSEHKEA 1w25A 83 :TALDGRG T0634 91 :IVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSD 1w25A 91 :RIQGLESGASDFLTKPIDDVMLFARVRSLTRFKLVIDE Number of specific fragments extracted= 6 number of extra gaps= 0 total=664 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w25A/T0634-1w25A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1w25A/T0634-1w25A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w25A read from 1w25A/T0634-1w25A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w25A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1w25A)S2 Warning: unaligning (T0634)H136 because of BadResidue code BAD_PEPTIDE in next template residue (1w25A)R137 Warning: unaligning (T0634)H137 because of BadResidue code BAD_PEPTIDE at template residue (1w25A)R137 Warning: unaligning (T0634)H138 because of BadResidue code BAD_PEPTIDE in next template residue (1w25A)M139 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRKNEGH 1w25A 3 :ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFKLVIDELRQREAS Number of specific fragments extracted= 1 number of extra gaps= 1 total=665 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l5zA/T0634-1l5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l5zA expands to /projects/compbio/data/pdb/1l5z.pdb.gz 1l5zA:Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 1l5zA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 1l5zA # T0634 read from 1l5zA/T0634-1l5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l5zA read from 1l5zA/T0634-1l5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l5zA to template set # found chain 1l5zA in template set T0634 2 :SLKKILIIDQQDFSRIELKNFLD 1l5zA 3 :AAPSVFLIDDDRDLRKAMQQTLE T0634 25 :SEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1l5zA 27 :AGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILAL T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYY 1l5zA 74 :DPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEKKRRLV Number of specific fragments extracted= 3 number of extra gaps= 0 total=668 Will force an alignment to be made, even if fragment is small Number of alignments=148 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l5zA/T0634-1l5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1l5zA/T0634-1l5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l5zA read from 1l5zA/T0634-1l5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l5zA in template set T0634 1 :MSLKKILIIDQQ 1l5zA 2 :SAAPSVFLIDDD T0634 13 :DFSRI 1l5zA 15 :DLRKA T0634 19 :LKNFLDSE 1l5zA 20 :MQQTLELA T0634 27 :YLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1l5zA 29 :FTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILAL T0634 74 :LKNVPLILL 1l5zA 74 :DPDLPMILV T0634 84 :SSEHK 1l5zA 83 :TGHGD T0634 94 :GLHSGADDYLTKPFNRNDLLSRIEIHLRTQN 1l5zA 94 :AIQDGAYDFIAKPFAADRLVQSARRAEKKRR Number of specific fragments extracted= 7 number of extra gaps= 0 total=675 Will force an alignment to be made, even if fragment is small Number of alignments=149 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l5zA/T0634-1l5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0634 read from 1l5zA/T0634-1l5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l5zA read from 1l5zA/T0634-1l5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l5zA in template set T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 1l5zA 3 :AAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILAL T0634 74 :LKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRK 1l5zA 74 :DPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEKKRRLVMENRS Number of specific fragments extracted= 2 number of extra gaps= 0 total=677 Will force an alignment to be made, even if fragment is small Number of alignments=150 # command:CPU_time= 30.850 sec, elapsed time= 107.433 sec. # command:DEBUG: alignment library has 150 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 150 # Adding 888 constraints to all_contacts Done adding distance constraints # command:CPU_time= 30.945 sec, elapsed time= 107.531 sec. # command:Reading probabilities from T0634.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 147.300 Optimizing... Probability sum: -219.913, CN propb: -219.913 weights: 0.529 constraints: 303 # command:CPU_time= 38.331 sec, elapsed time= 114.987 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 303 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 303 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 585 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 585 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 38.345 sec, elapsed time= 115.928 sec. # command: